Kamui can't warp Rikudo enhanced Susanoo just like Kakashi can't ghostify his Susano'o.
Madara doesn't have the Preta Path - he doesn't know the name of Nagato's absorption. He doesn't have any of the paths.
Tailed Beasts were a narrative device for the authorian intent or they probably encountered an Edo in thier lifetime. The key factor emphasized in that juncture when they said that, was "blood" and we are aware of the fact that lifeforce is contained in the blood; a hint to this fact being Uzumakis possessing high amounts of lifeforce and coincidently having thier hair dyed red symbolizing former. Lifeforce being a predominant factor of a person's overall power; the ANBUs' commenting how they (Edo Hashi and Tobi) were slowly regaining thier lifeforce -meaning- they were consequently gaining in strength, which goes in line with the fact that Orochimaru perfected the Edo Tensei.
Sasuke trapped them (WZs') in Genjutsu, with Itachi's eyes, the man hyped by the alliance HQ authorities regarding his supernatural Genjustu-control abilities on par with WZ's masquerading-sensor bypassing capabilities, and was thier only known theoretical explanation prior to the revelation of latter's play in the fact.
WZ not attacking Sasuke goes in line with the statement he made prior to engaging former. That "Itachi's power permeated all throughout his physique" upon transplanting latter's eyes. Probably warded off the Zetsu from overtaking former.
Limbo never used Ninjutsu to begin with. Learn what a nerf means. Something that happens which contradict's a fighter's pre established feats of power or capabilities; illogically. That's a nerf.
Kamui doesn't work on Juubi Jinchuurikis. Just like Kakashi couldn't warp Kaguya instead had to physically pierce through her directly.
Hashirama possess an inbuilt resistance to Genjutsu, + he possesses one of the powerful Genjutsu in the verse, that a master of illusions couldn't break (Hiruzen, who mastered 1000s of illusions, by Ebisu's words.).
RSM is basically a Jesus-Mode that asspulls it's way through anything; Naruto mastered flight without him even being aware of the fact. + instant comprehension of all things means he unconciously decipher's the loop-holes of said Genjutsu and break's out of it; unconciously, without being aware of the fact of course. The mode transcends the realm of logic and reason; he recreated Kakashi's eye without even being aware of the technicalities behind said recreation. IT is probably the only Genjutsu that could even remotely affect him as per canonical implication.
The Divine Tree required the individual life energy of it's victims, Edos don't have a physique; therefore no LE. Only the soul and ash as replacement for a physique.
Kyuubi Chakra Modes are unexplored poorly explained territory. Like asking how the Sages Tools came into being or the Nunoboko came into being. The design manifesting on cloak resembles the Uzumaki Clan Symbol and Sarada's MS; former of which being unexplored territory in of itself.
Gedo arm being decapitated means there's no existing link between the main body; given the thing by itself isn't a Bijū but just the shell and the concentration of the bijū chakra is located in the eye area; seeing as an eye appears when a bijuu is sealed and Kakashi thought ripping off it's skull meant it's dead, given the chakra that gave the thing some sort of conciousness, seperates from the main body, altering it into a lifeless doll in the process.
The Seals would seal her instantly hence why she backed off. A single touch is all
that's necessary to initiate said sealing.
Hagoromo giving powers doesn't necessarily mean he was at full power, just like Orochimaru isn't at full power even though he could distribute the Curse Marks throughout his subordinates, using said power Sasuke managed to even beat him - the originator of the power. In a similar fashion to how Jugo the progenitor of said Cursed Seal was former's subordinate.
Asura and Indra possess halves of Hagoromo's power hence they don't possess conciousness given latter is a higher-up Otsutsuki ability - a trait only replicated by Momoshiki, who is an elite and peer to latter. Former are diluted in Otsutsuki blood.
Obito was a sensor as a Jubi-Jinchuurikir; he probably retained the ability, or it could've been authorial intent.
Madara's Jubi Powers are a piss ant compared to RSM Conjuctioned with considerable Bijū Power because it's a supernatural mode that's used in conjunction with Bijuu powered attacks; whereas former is simply Jubi Senjutsu powered.
Sasuke sensed Naruto gathering a huge accumulation of Natural Energy; and the keyword here is "huge" -meaning- he had to retaliate with something even to balance out the impact or else he would've been overwhelmed by the resulting explosion going his way.
He thought BZ was his will; if latter had straight-up told him the underlying methods to achieve the Rinnegan, he'd simply be digging his own grave as he no longer can fool him into thinking he is indeed his will. He needed to manipulate the guy into achieving the IT Plan.
Madara's arsenal wasn't limited, it's simply the consequence of achieving a new power. Like Obito couldn't utilize Kamui because of the Jyubi inside him. Specific power accumulations give rise to specific power limitations, consequently - and it's not plot or any bullshit like that - but simply an in-verse consequence of wielding the technique or ability.
Edo Hashirama was not at full power as Madara explained; neither were Tobirama.
He (Hashirama) already has chakra greater than 2 Perfect Jinchuurikis (Minato, and Naruto.) and Kurama was stated to possess limitless amounts of chakra back in Pt.1. What'd gaining another set of unlimited chakra accomplish? Worthless to someone like him seeing as he sold the Bijū to the neighbouring lands to maintain peace.
Again, learn what a nerf means. Fukasaku flat out states Naruto surpassed every other Sage before him. A sillhoutte of Minato appears. So he can't have the same level of mastery as Pein Arc Naruto even.
RSM + Boil Release = Kaguya's .
Hagoromo couldn't personally visit him due to the Bijū Chakra not being accumulated into one place, in conjunction with Indra and Asura's Chakra, as per his own words.
Certain techniques in the Narutoverse elude chakra-absorption, e.g., Itachi's Amaterasu, Raikiri, Chidori, Six Paths techniques (Onyx Chidori, Sand Sealing Rasengan); RSM Rasenshurikens seems to be a part of that group.
Sasuke had Amaterasu; something BZ was scared of. Enton is also a threat to her Ice dimension. He's physically quicker, in addition.
Kaguya isn't capable of using it (Izanagi) because Hagoromo invented it.
OT: All of these wtf moments can be explained one way or the other, using in verse implications; and if it can't be, it's simply unexplored territory that'd be explained when it becomes relevant to plot.
