As an example of some other laziness recently, We've seen that Tobi can apparently resurrect the Juubi WITHOUT capturing Naruto or Bee first. That opens up some major plot holes, and makes Tobi look like a gigantic idiot when he's supposed to be this genius schemer. And if Tobi is a gigantic idiot there's not a whole lot of suspense because compared to "heros" and "geniuses" like Naruto and Kakashi, an idiot cannot win so there's nothing to worry about. HOWEVER, we accept this shortcut because it seems like Kishi has a larger story to tell and he's cutting some corners to rush the story to the important ending. The important part is not that Tobi is some genius mastermind, the important part is that the Juubi is resurrected, creates an existential threat, and Naruto is one of the only people in the world able to save the day.
Back to topic: One of the big themes of the manga, from the very beginning, is that The Will of Fire (the desire to help and protect the people you care about) is what makes a ninja truly strong. This is why Orochimaru could not win, even though Hiruzen died. This is why Naruto was able to unlock his hidden power and Save Sasuke on the bridge. It's why Naruto was able to defeat Kiba AND Neji in the chuunin exams, two ninja who were supposed to be way above his level. It's why Naruto was able to defeat Pain, and it's why Naruto keeps pursuing Sasuke and refusing to give up his attempt to redeem his old friend. It's why Hashirama defeated Madara, and why Super Edo Madara with Rinnegan Version 2 STILL considers Hashirama to be his equal or better. In short, this idea of the Will of Fire IS THE ENTIRE MANGA. The idea is that the Will of Fire is the source of true strength, allowing an "idiot" like Naruto to defeat some of the most powerful enemies and some of the most over-powered techniques in the entire world.
Obito is a person who apparently had the will of fire. So did Itachi and So did Shisui (I mention these because apparently the Uchiha are the source for the alternative, the Curse of Hatred).
Pain was engulfed by the Curse of Hatred until he met and fought Naruto. At that point, Pain's viewpoint changed to the Will of Fire, he brought everybody back to life, betrayed Akatsuki, and died as a real hero with a smile on his face. Konan, likewise, was a founding member of Akatsuki, but gained the will of fire and died to protect the people she lived (or, to protect their memory and the respect due to their corpses). Also, at the time Konan represented the single largest threat to Tobi, injuring him significantly and causing him to sacrifice one of his precious sharingan eyes.
Look at Pain's story more closely: He was trained by one of the "main line" Konoha ninja, Jiraya. I say "main line" for people who are in a direct teacher/student relationship chain that links all the way back up to Hashirama. Pain was trained by Jiraya who was trained by Hiruzen who was trained by Hashirama. I'll talk more about this later. Pain should have been a good guy, because he was trained by one of the good guys. However, Pain experienced some pretty bad things, was manipulated by Tobi and became a bad guy. Now look back at Tobi. If Tobi is Obito we have the same story. Obito was trained by one of the "main line" Konoha ninja (Hashirama->Hiruzen->Jiraya->Minato->Obito) so he should have been a good guy. His last words and actions do indeed suggest that he was a successful recipient of the Will of Fire. However, he clearly turned into a bad guy which means at some point he must have been manipulated by somebody else who was a bad guy (Madara?). That's the same exact story, and it's extremely lazy for Kishi to do the exact same thing with two completely different characters.
If Tobi is Obito, then the will of fire is just something that can be discarded for no good reason. Even though Obito had the will of fire, and taught it to Kakashi (and Kakashi has CLEARLY become very powerful because of it, and Naruto even more so), Obito gave it up for no stated reason and somehow became more powerful than Naruto and Kakashi combined. That seems to contradict the idea that The Will of Fire is more powerful than the Curse of Hatred. The idea that Obito went from being a major source of the Will of Fire to becoming a major source of the Curse of Hatred, all while inexplicably faking his own death, is a really hard pill to swallow.
Further, if it is Obito, the entire story has gotten extremely small. The whole plot is, essentially, one of Minato's students (Obito) versus another one of his students (Kakashi), and Naruto is just a representation or avatar of Kakashi's world view. The story should have been renamed "Kakashi" since he's the star, and his friend is the enemy, and his sensei's son is his student and almost nobody else really matters. Look at the teacher/student relationship tree from Konoha alone, divided by teacher/student "generation". This is the "main line" of Konoha ninja that I mentioned above:
1) Hashirama (the most powerful ninja who ever lived, founder of Konoha, the source of DNA magic which is powering Zetsu and Akatsuki, Arch-nemesis of Madara, direct descendent in DNA and Mindset from the Sage of 6 Paths) and Tobirama
2) Hiruzen (Third Hokage, Major influential figure in Konoha over two wars and several decades, student of Hashirama and Tobirama), Danzo (also taught by Hashirama and Tobirama, a shadowy figure who was behind several major events and problems in the manga)
3) Tsunade (Fifth Hokage, major general in the allied shinobi army, world-famous Sennin), Jiraya (Considered for position of Fifth Hokage, world-famous sennin, sensei to both Minato and Naruto, Sensei to the ame orphans, who would later go on to found Akatsuki), Orochimaru (Major villain of Part 1, Major "third power" actor of part 2. Mentor to Kabuto AND Sasuke. Enemy of Konoha and Akatsuki. Founder of his own hidden village. Attacked and nearly destroyed Konoha once, has plans to try again)
4) Minato (Student of Jiraya, Fourth Hokage, Father of Naruto, Husband of Kushina, single-handedly helped to win the third ninja war. Considered one of the strongest ninja of his time), Nagato (Student of Jiraya, has the legendary Rinnegan, Founding member of Akatsuki, leader of Amegakure, invaded and destroyed Konoha, helped capture and sealed the first seven bijuu, the only ones Tobi currently owns), Kabuto (accomplice and student of Orochimaru. The "successor" of sorts to Orochimaru's research, techniques and motivations, a major enemy and accomplice to Tobi in the second half of part 2, The source of the Edo Tensei technique as used in the war, which allowed many plot threads such as unresolved issues between the living and the dead to be finally resolved)
5) Kakashi (Student of Minato, favored candidate to become Sixth Hokage, legendary world-renowned hero of the sharingan), Obito (Apparently he's Tobi now, the major enemy from Part 2, started the fourth great ninja war by himself, resurrected the Juubi by himself, has plans for world domination that the entire allied shinobi force is having trouble combating).
6) Naruto (Student of Kakashi and Jiraya, Primary series protagonist, some sort of legendary "reincarnation" of the sage of 6 paths, subject of several prophecies, Owner of the most powerful of the 9 Bijuu, war hero), Sasuke (Whiny crybaby that fanboys love. Also he's been a major focus of the plot even though he's just a pawn that other, better enemies have used and abused).
I'm going to call this list the main line "inheritance path" of the Will of Fire. Hashirama has created that idea and passed it down from teacher to student through 6 "generations" to Naruto. Some people didn't get the message along the way (Orochimaru, Pain, Sasuke), and some people got a really weird version of the message (Danzo), but that doesn't mean the message wasn't there.
I would include Itachi in that list as well, but I don't know who his sensei is (was it Danzo?).
You see what I mean? In only 6 "generations" of Konoha student/teacher relationships, there are direct relationships between ALL of the major heros and enemies of the entire manga, past and present EXCEPT Madara. That part is important. Madara is the only person who represents a completely separate lineage, and a completely separate alternative world view. The big question is this: Is Tobi a direct recipient of Hashirama's world view and it got corrupted (same exact thing that happened, in different degrees, with Danzo and Orochimaru), or is Tobi a direct recipient of Madara's world view? Which of these makes more sense?
And before somebody speaks up and says "but there were other enemies in the manga who weren't part of this group", let me stop you right there. The rest of Akatsuki were just temporary fodder ninja and are all dead. None of them played more than a temporary role in the manga. The rest of the "Konoha 11", who played such important roles in part 1 have basically all become fodder ninja as well, mixed up in the larger war effort and not doing anything special or playing any important roles in the plot of part 2. Almost no other ninja in the entire manga has any sort of backstory at all.
This is the problem with Kishi's storytelling so far, and it's a problem that will get even bigger if Obito turns out to be Tobi: All the major players in the war are connected to each other. The whole idea that it's a world problem, and that all the ninja villages are in this together is crap. It's a Konoha problem, between a very small set of elite Konoha ninja. Has any other village contributed to the major plot of the story so far? Barely, if you consider that Akatsuki was founded in Amegakure by residents of that village (as motivated by Konoha's actions in the second world war, and as trained by Jiraya). So even in cases where other villages have played any part, almost all of it was motivated and encouraged by this small set of Konoha ninja. We can extend "almost all" to "all" by including Madara in this list. Think about that. Not a single major event, IN THE ENTIRE WORLD has happened in several decades that wasn't directly or indirectly caused by Hashirama and his followers, or Madara himself. That's a pretty small world.
So if this list above is the major inheritance path for the Will of Fire, than Tobi=Obito implies that there's a major flaw in that ideology. However, IF Tobi is somebody else like a relative or student of Madara (the local originator of the Curse of Hatred), that helps to broaden things up a little bit. At least in that case, there isn't a direction teacher/student relationship chain between Tobi and Hashirama, but there could be a direct one between Tobi and Madara.
IF you consider that Izuna is basically on the level with Madara, and other Uchiha (Fugaku, possibly Kagame) have inherited the Curse of Hatred from Madara through these kinds of relationships, then you show a clear lineage. Madara and the people who follow his lessons are the bad guys, generally. Hashirama and his followers are the good guys (with several BIG exceptions). Madara And Izuna are the central points of the Curse of Hatred, and they help to "infect" other people around the world with that message (Akatsuki members, predominantly). Even though Madara and the Uchiha were also from Konoha, this helps to expand the story and make it seem like things are a little bit bigger and the whole world really is involved in this war.
So that's the problem with Obito being Tobi. It makes this whole big world war into a very small clan conflict that a lot of other nations are involved in for no reason. It also shows that Madara and Tobi (an avatar for Madara for much of the manga) have no direct relationship, which raises the question as to why their motivations are so similar. Pain was clearly motivated by Tobi so there's a clear relationship there. Orochimaru wasn't motivated by either Tobi or Madara so even though Orochimaru is a bad guy he's a bad guy for his own reasons. By having Tobi be somebody who HAD the will of fire AND WAS a direct recipient of Hashirama's teachings through a direct teacher/student chain, that just muddles the entire story and makes all the themes from the entire manga meaningless.
By the way, some people will point out that Sasuke was also a direct teacher/student recipient of the Will of Fire, but seems to be an embodiment of the Curse of Hatred. Well, not really. Sasuke has been heavily manipulated and lately seems to want to make his own decisions. If anything, Sasuke is more an embodiment of Orochimaru's third option, being a criminal with dreams of personal revenge and gaining personal power, without actually buying into the Curse of Hatred as Madara and Tobi know it. Tobi WANTED Sasuke to follow the Curse of Hatred, but Sasuke is instead picking a third option and following Orochimaru.
So basically, there are three "schools" in the manga:
1) The Will of Fire ("peace through love and understanding")
2) The Curse of Hatred ("peace through conquest and power, also get revenge on the Senju")
3) Orochimaru's third way ("conquest and power through research, forget peace. Also, get revenge against people who wrong you")
Saying that just about ALL the villains and heros and main characters of the manga come out of the first school, but the enemies are suddenly pretending to follow the second school is kind of lame. It was fine when Pain did it, because he's just one person who was easy for Tobi to manipulate. To say that Tobi's story is basically exactly the same as Pain's story is kind of lame. And then to say that Tobi tried the exact same thing on Sasuke, but failed, is even more lame. If Tobi is somebody who is legitimately part of the second school, that helps expand things and helps to make the conflict more real, and makes the division between people more obvious.