There are a few things I don't like about the series:
Too much limited content. "Oh, you think that Pokemon's cool? Well too bad, because you have to give it this item and trade it with someone then trade it back to yourself to obtain it". Like, seriously, what even is the point? Would it hurt them to make Pokemon evolve just by levelling up holding the blasted item instead? Also, "Oh, you want a Leafeon? Well too bad because Moss Rock doesn't exist in this game."
The "rare" encounters in B/W... When they say that, they're not kidding. I swear, I've come across more shinies naturally than I've come across those guys.
Roaming legendaries, you can simply never be prepared for one to smack you in the face.
Also, the whole competitive scene is ridiculous. EVs and IVs? Too tedious. Give me a nature, gender and ability, and that's about all the micromanaging I could care to do.
Breeding is fine to get a good egg move, but how am I supposed to know what egg move I want, and what Pokemon I want it on, and what its father should be if I want it to learn said move? Far too complicated...
Pokemon used to be enjoyable using only basic knowledge of the game's mechanics. Now there's so many weird things to do, and even more limits to what you can do within an actual, casual gaming session.