You can understand the complexities of the move and still not like why the move was done.
This was particularly souring because the entire point of the move to models in XY was to futureproof such that the amount of work on animations from models in Gens VI and VII, would be minimized vs. having to do every single remodel, reanimation, etc. This is why people were okay with the performance shitting the bed at times in the 3DS games, because the idea was that somewhere down the road, the games would ultimately come out of it much better. Furthermore, Game Freak invited scrutiny by saying that (and I'm aware this is translated, so I take a portion of it with some grain of salt):
The scrutiny came from the fact that the graphics weren't exactly up to par for the amount of Pokemon that were cut from the game. I've said it time and time again, if Game Freak had simply left it at saying "too much Pokemon", people would still be mad but they wouldn't go off and scrutinize every single pixel to make them look like fools. So I do think Game Freak deserves some criticism if only because their claims did not measure up to reality. If not this translation, then it was the USGamer interview where Masuda said:
Additionally, I do think this is a symptom of a problem with the Pokemon franchise. When iterating the games, Game Freak never really had the foresight to think about rotating out a roster of Pokemon per game (even though the franchise pattern basically writes itself: feature the new region's Pokemon and select a rotation of returning Pokemon and leave it at that without enabling return of ALL Pokemon). The reason why Digimon gets away with the rotation is because they never stuck with the growing roster for every game. Not to mention, Digimon tends to do a great job at the amount of Digimon added based on nostalgia and newer At the same time, Digimon's battle system is a lot simpler than Pokemon's, so there's less focus on the series.