Uh, no? In comparison to how prepared Kiritsugu and Tokiomi were for the whole Grail War, Shirou and Rin fall pretty flat on their back. Granted, Rin was prepared to a point, but no where near as much as Tokiomi who planned a swift win along with Risei and Kirei. Rin more so was only prepared in terms of her own battle skill, but nothing else. She wasn't particulary mentally prepared for the fight which was said in the visual novel more than once; such as her not coping well with the casualties of others and over-all screwing up in the most crucial moments whilist executing other less important moments absolutely perfectly.
Shirou, on the other hand, was not prepared at all for the war unlike Kiritsugu. Kirei didn't prepare for anything either other than becoming Lancer's Master unlike his whole team up with Tokiomi in Zero. Although, he was more so forced into it.
I don't really know where you get this ''they are one-dimensional thing'' for Stay Night's character because they all had different sides to them and had more human-like reactions, emotions and such things unlike Zero's cast. For an example, Kirei in Zero was just trying to find an answer for his birth and what he should believe in Zero while in Stay Night, you could enter his whole inner conflict through his flashback of his earlier life and how he had the common sense of a human that was raised as a fine human being, but was defective from birth and his sense of beauty was different from other human's - how he doesn't find ordinary, good things beautiful like normal humans do. Kirei in Zero was just searching for his answer like Kirei described himself when he was young in Stay Night. However, you get to read through his whole philosophy as a human and dark view point of the world along with his full inner conflict and what he believes is right and what is not - what he finds beautiful.
Shirou also had much more sides to him than Kiritsugu did. For an example, Kiritsugu killed his emotions and focused on playing the villain whilist holding a heroic wish that he intended to wish upon the Grail and change reality itself. You never really get in depth with him too much or how he acts as a person during the situations that are not connected to his ideal. However, Shirou, on the other hand, is someone who is presented to you as a likeable, naive guy who chases after a naive wish to save everyone. It presents to you an altruistic view point on how Shirou seems to anyone who's viewing him from outside; a kind, good hearted boy who wants to save everyone. However, once you view the world through his world and enter his inner conflict, Shirou's characterization presents to you an extremely realistic view on the topic of heroism unlike Kiritsugu's. He's characterized as someone who has no sense of self and acts on down-right suicidal lines of thought and actions. He is presented as someone who would save everyone even if he has to sacrifice himself to the point where he acts down right suicidal, but the real reason he acts as such and wants to save everyone is because ultimately he is extremely selfish. He only gains happiness when helping others. As long as others around him are happy, Shirou is happy as well. He helps and wishes to save others and acts suicidally to obtain his desires ultimately to gain his own salvation; his own satisfaction. He is someone who has absolutely no love for himself, a suicidal person with no sense of self, but yet he is extremely selfish.
More so unlike Kiritsugu who is presented as someone more robotic - killing his emotions - Shirou is presented as someone who acts extremely humane, but is far from it. He lacks normal human function to the point where he is acting borderline sociopathic - Heightened cognitive functions. Diminished emotional comprehensive response. NO emotional response to certain factors - himself. Examples would him be having absolutely no human reaction to people dying unlike Rin who couldn't even operate normally because she was too disturbed and afraid of dead bodies. He acted like a machine to the point where Rin asks him how could he remain so calm about such things and his only response was that he was used to seeing dead bodies. He's also genuinely puzzled at most humane function and feelings, such as him not understanding what was wrong with sacrificing his own self by commiting suicidal acts to safe others while Rin got furious or sad for him or another example would be his uncapability to grasp honest feelings of action - no, that is not the usual ''dense mc'' case, he is genuinely uncapable of grasping such basic human function. And yet another example would be his lacking in emotion reaction to hearing about Sakura being a rape victim and Kiritsugu being a cruel Master in the last War, instead he just reacts to it all as if he had seen it all coming; as if it was a part of his calculations. Normal people wouldn't react like that. Shirou has absolutely no emotions regarding his own self and most of social interactions he has are done via predicting the accurate reaction or trying to solve the situation.
Just like Kirei, Shirou anticipates and acts as a human. Which is the whole point at the end of Heaven's Feel that Shirou and Kirei are the same in that sense. They both have a wish that can only be granted by the hands of others and they are both far removed from the function of a normal human and only act as one in order to fit into society. Shirou follows "social norms" as long as they fit his view. Otherwise he says what he wants resulting in pissing off people
Another point that brings us back to the topic of altruism is that Shirou is painted as a genuinely good person only from the outside. In the inside, Shirou is someone who is far removed from the morality of normal humans. Remorse - Shirou's remorse is only existing within his ideals - you cross that boundary, you do not get that from him. Example would be how he felt no remorse for almost killing Shinji - if he wasn't interrupted - in the Fate route despite Shirou acknowleding Shinji as a ''friend'' multiple times in the beginning just because Shinji did not fit his ideals and his actions were something that acted against them. Shinji told him he had no guilt for what he had done and Shirou had calculated it as if that was the path Shinji chose to walk down on, thus deciding to remove him because he was a threat for his ideals. Another clear example would be Kirei. Do I really need to say anything about this one?
You could in fact slap two alignments to himself. The first one would be neutral good for his ideals that he follows in order to save everyone. The second one would be on Shirou himself; chaotic good. Why? Because no matter how you look at it, Shirou's wish is chaotic and his way of becoming a hero is chaotic. A part of Shirou wishes for a clear evil to happen - evil is destructive which means Shirou is wishing to prove his worth as a hero through destructive means by wishing for something destructive to appear so he could eliminate it - so he could commit said heroic acts and become a super-hero, gaining his own happiness. He's extremely violent - spent his whole childhood beating up bullies because he thought that's what a hero is supposed to do and casually says how he should give Shinji a beating for hurting Sakura.
More so what once again makes Shirou a lot more interesting than Kiritsugu is that he is written like a sword rather than a person; which is why his Origin is ''Sword'' after-all. His characterization and a sword's attributes have a lot of stuff in common; such as that a sword can be heroic when wielded by a swordsman with heroic intentions - Shirou's swordsman in this case are the heroic ideals he up-helds - but ultimately the way this sword goes about commiting heroic acts is in a destructive - violent is a better word to use, but destructive is more appropriate for my point - way which is a nod towards how Shirou wishes for a clear evil to happen.
A sword is violent very much like Shirou is.
A sword is ultimately meant for offensive acts rather than defensive acts - while it can defend, it is not a shield and is meant to attack rather than defend - which is, in my opinion, a nod towards Shirou's suicidal nature and how his whole fighting style is about him leaving obvious openings in his attacks so he could know where his enemy would strike which he would use as an advantage. It's a suicidal fighting style only Shirou could pull off.
A sword's actions are manipulated by a swordsman much like Shirou's actions - the sword - are manipulated by his ideals - the swordsman. Etc. There are many more examples as why he's just a weapon that is wielded by his ideals rather than a person who bases his actions off of his own choices.
Okay, let me get back to the topic of how Shirou's characterization unlike Kiritsugu's gives us a more realistic view on the topics of altruism and heroism. While Shirou seems like a good, determined person from the outside who just wishes to save other people because of his own good will, we learn that he's quite warped in the inside and there's a whole new content of reasonings behind his wish to save everyone. In other words, his heroic acts are altruistic only from an outside point of view while his real reasoning for saving everyone is in fact to obtain his own selfish happiness. This is why Shirou's character is an extremely realistic view on the whole topic of heroism; people do good acts because they feel good about doing them. It's just that the acts of heroism seem altruistic from the outside, however are not altruistic when we know the person's real reasonings. His characterization tackles the topic of altruism and heroism in a rather very realistic way, which most heroic characters from other series fail to do.
Shirou doesn't fight for the ideals of wanting to save everyone for the actual sake of saving everyone. While he does believe that saving everyone is a good thing - and it is a good thing - Shirou more so up-helds his ideals for his own salvation. For an example, if strangers were to die in front of him, Shirou wouldn't be angered because lives were lost. He would be angered because he couldn't up-held his ideals and be an ally of justice, thus ultimately being uncapable to attain his own happiness as his happiness only comes from suicidal-like actions such as saving everyone and putting their lives' importance over his own.
To put it blunty, Shirou's characterization is the deconstruction of the shounen hero MC troupe. He shows us that the whole heroism thing isn't as simple as it seems and it really isn't something altruistic. Kiritsugu all fails to do this. He is more like a machine and just takes the general role to make himself the villain. Unlike Shirou, he doesn't really accept failure either until a tragic event happens - the fire. Shirou accepts that he can't save everyone in UBW, but will still try to do so and save as many as possible because it's a beautiful wish to pursue. But it's more a case that Emiya Shirou's existence isn't possible outside his ideals. After-all, a sword needs a swordsman to wield it. Everything he does ranging from his emotions and actions are controlled by his ideals. Even in Heaven's Feel when he betrays his ideals for the sake of saving a single person as a normal human would do, Shirou cannot work outside his ideals. He still tries to save Illya, Rin - regardless if she was his enemy at that point -, and chooses to sacrifice himself at the end of HF to save the city from getting destroyed by Angra Mainyu instead of running away with Sakura and leaving the task to the Magus Association. Even in the end, he chooses his ideals over Sakura's happiness even if he does choose her life over his ideals.
Because Shirou cannot exist outside of his ideals. Emiya Shirou who does not help others cannot exist. After-all, his ideals are his world. The person Emiya Shirou can try to exit the world by straying away from his ideals, but he can never truly exit the world because then his existence ends. And even then, in UBW it is pointed out how the world that the weapon named Emiya Shirou exists in is a fake one. One that cannot become reality - his ideals cannot be made into reality - and one that is not even his own; just a world he borrowed from another - Kiritsugu's ideals.
There's a lot more to say about Shirou, but I'll stop here. Every F/SN Master and Servant is better characterized than their F/Z counter-part and I can expand upon it, of course. Now let me tackle other things you seem to misunderstand.
I don't understand. Zero's characterization for said two characters is directly taken from the VN. It is exactly the same for them. Except that Stay Night goes into depth into them and expands upon them; their world-view, philosophy, ideology, etc. I've explained how Kirei is a lot more characterized in the VN and I can do the same for Saber if needed. Gilgamesh is also a lot more expanded upon and you can view his contrast - as a hero of the old age - with Shirou - as a hero of the modern age. It's shown to you how Gilgamesh would be considered evil in this era because his term of heroism is way too cruel for today's society and would more likely be called a villain rather than a hero like in the old ages.
The characterization is a lot weaker than Stay Night's. For an example, FSN Rider's characterization goes deeper than Zero Rider's characterization. It's explained to you how she became a monster and how she chooses to protect Sakura over anything because she sees her as a younger version of her own self - she chooses to protect Sakura because she was uncapable to protect her own self. Rider does go into his kingly philosophy yes, but his dream for wanting to reach Oceanos or his own characterization isn't just as expanded upon. In fact, he kind of critizes Saber for not being able to attain her wish nor be able to let go of it when he himself kind of does the same with the Oceanos thing.
No, the whole Grail War is a SECONDARY problem. Fate/Stay Night is a story about Shirou and his world-view. It focuses on his psychological state and his ideology; it is viewed from his point of view. How he reacts to the events of the war, how he views the world, how his relationships with others shape both him and others as well as his view on heroism is the topic of Fate/Stay Night. Altruism and heroism. That is it. It all shows you different shapes of heroism through different characters and it shows you everyone's personal inner conflict and how they act in response to Shirou and the topic of heroism.
Zero is not meant to be a stand-alone story. It is a greek tragedy type of story. A bunch of thrown-in elements racing towards an already pre-determined outcome. It enriches the Fate/Stay Night story and shows you how it all led up to the start of the event that started Stay Night's story - Fuyuki fire. It is not meant to focus on characterization unlike Fate/Stay Night which is a character story - builds a story through it's character's world-views and inner conflicts. I'll give a clear example. Think of a detective movie about a murder. The whole movie is spent gathering evidence, clues, etc. and such things and then at the end of the movie, the investigator sits down and is like ''Alright, this is how it all went down...'' <- explains how the murder happened. Zero is the murder at the end of the movie while Stay Night is the story. Zero is only meant to enrich it and it depends a lot on the context from Stay Night.
Atleast he isn't ignorant and clueless about the actual world
