I think what people had issue with II was that it was too different gameplay wise, at least from I and the conventions of other RPGs from the time and eventually the rest of the FFs. Not to mention, at least back in the NES era it had many ideas, but the implementaton was kinda rough in many ways, however the ideas weren't bad per se and could be used for good effect as seen with the SaGa franchise.
Story wise we got the Emperor, honestly a pretty underrated baddie in the franchise. Sure, a by the numbers evil overlord, but boy an effective one at his role.
Regarding After Years, IIRC given it was released as a mobile game in early 2000s I think, it had to reuse a lot of assets from the original game and be released in small episodes, hence many repeated elements and so many scenarios, but honestly it's pretty ambitious for a game of the era on phones so long before the market we have now.
I think XIII suffers from the backlash just all big franchises have by this point, we always need a scapegoat for what's perceiving what's wrong and treat it as the worst mistake of humanity. I mean, I do think XIII has important flaws, but nothing that makes it unplayable or anything, not to menton, as soon as XV rolled along, opinion softened on it and XV became the target. If you ask me, when the fanbase grew, opinions split, decisions became increasingly more controversial because of it. Though production issues at Squeenix are thing I am not gonna pretend those don't exist.
To be very honest... I actually have liked every FF game I've played, even spinoffs. The closest thing to disliking one was Dirge of Cerberus, but in the end I kind of saw a So Bad It's Good appeal to it and still had fun with it, despite I wouldn't call it a good game.