How much better do you think Part 2 Naruto would have been if Pain wasn't so full of faggotry and only revived Jiraiya and/or Kakashi,
Seems a bit difficult to pull off when there'd be no reason for him to only revive 1 or 2 people unless the Rinnegan's power was far more limited. In the case of the latter, it'd make the Pain Arc a fair bit better (even if still a poor man's version of most of DBZ's arcs), though it would probably be easier to just write out Pain's revival powers in general.
Itachi was brainwashed through Danzo's Kotoamatsukami to commit the atrocities he did,
Removing almost all his character agency could end up being as bad as having nonsensical motivations, so it'd be a difficult route to write well, particularly with him not reaching out to inform Sasuke very early on (assuming the mind control broke soon after and he wasn't just Danzo's puppet throughout, which would cause even more problems). In order to make this rewrite a vast improvement, it'd have to be established that the guilt he felt gave him a sense of self-loathing and disgust for his weakness and have him set Sasuke up to kill him as a form of repentance, as well as his motivation for joining Akatsuki being to take down Danzo. Itachi's characterisation would still end up being generic, but better than a contradictive mess.
Obito was infused with a Black Zetsu-like entity to make him follow Madara's will
Again, difficult to pull off mind control well, not to mention getting a bit repetitive if two major villains were GASLIGHTED by jutsu. It would be better to stick to him having agency and being corrupted by his own sufferings, but with the focus being far more heavily on the perfect illusion aspect of his plan than just "muh Rin".
Juubito was defeated through Madara's will regaining control when he was about to lose to Naruto and Sasuke (forcing him to resurrect Madara without him being talk no jutsu'd first and eliminating that royal "coolest guy" cringe),
If we had to do this without Obito's agency being removed entirely, I could see the idea of Zetsu latching onto him and reviving Madara through some jutsu working if fleshed out, or having Madara remain a decrepit husk throughout most of the war with Zetsu gathering chakra to restore him. Still pretty generic, but better than what we got.
Either way, the "Obito was the coolest guy!" speech can be entirely removed regardless of how you rewrite it, since it does nothing but destroy Naruto's characterisation.
and Kaguya's resurrection was an unintended consequence of Juubidara being too badly wounded to keep the Juubi inside him in check?
That'd be slightly better, though it would probably be best to just remove Kaguya's active role in the plot entirely with how she just came in at the eleventh hour with only one statement to act as a poor attempt at foreshadowing.
Overall, it'd most likely be a step above something like Part 2 OP, though still likely no more than average at best with the many other problems within Part 2 Naruto (elemental release training being brought in too late, the Sai Arc being complete filler, Neji's "flawed" belief being proven right, etc.).
As icing on the cake, let's say Studio Pierrot and Shueisha also don't milk the series with Burrito.
That's something everyone can agree would be a vast improvement for the franchise's legacy as a whole
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