Pretty much every single criticism of this game that I've seen is something that I would've never noticed while playing, in comparison to other Pokemon games where there's always that one major flaw that plagues the entire run. Hell, all the main criticisms of this game are points that I think it does a lot better than other games in the series.
>Difficulty
Although not perfect, it had the right idea. It is true that a lot of the gyms get steamrolled and the EXP Share is overtuned, but in Sky Battles, Inverse Battles, Restaurant Battles I have to use actual strategy, and the game has plenty of challenge in the postgame thanks to the Battle Institute and all the different formats in the Battle Maison where I have to use actual strategies instead of spamming the strongest attack.
>Kanto pandering
This one I just don't get at all. I have a completely different team full of Pokemon from different gens every time I play through XY. You get a ton of options even before the first gym, and you're still finding new Pokemon at the end of the game. All the Kanto Pokemon handed to you are completely optional to use.
>No postgame
No, not really. First you get the Looker storyline, which is a few hours of extra story content, then you have multiple battle facilities such as Sushi High Roller, Battle Institute, and Battle Maison which easily have hundreds of hours worth of replayability.
>3D Pokemon
I just don't see how this is a bad thing. The Pokemon are more faithful to the source material than before, and they have way more expressive animations that are context specific based on what's happening to make them way more lifelike than the sprites ever came close to.
Anyway, why exactly is this game hated nowadays? It's not perfect, but I personally think it's the closest we've ever gotten to a perfect Pokemon game, and I've played them all.