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What this gen got right is what the series has been needing for a long time in my opinion - personalization.
The whole series is about going on a journey with a team and gaining bonds with them, and this is repeated in dialogue and themes throughout every game. But there was just always this sort of disconnect - you were playing as a kid, you were using a bunch of barely animated sprites, and your Pokemon were limited to a very small amount of animations if any at all.
3D models characterize everything so much better. Everything looks more real, in the sense that things move more naturally. This picture for example. You couldn't realistically get this kind of detail of movement on every Pokemon with spritework without a fucking immense amount of man power and time. With 3D everything is this detailed and moves so much more naturally.
Amie also helps towards making things more personal, since it makes the interaction with your Pokemon much more special. Your Gengar isn't just a Gengar. Getting another Gengar with the same moves won't just mean it'll only be different in IVs or EVs, but it'll also treat you differently than one that you've spent time with in Amie.
And obviously, trainer customization makes everything more personal by letting you choose what the protagonist looks like and wears.
The games aren't perfect, but holy fuck did they get that "personal" feeling right this gen. I can forgive poor optimization for that.
