It may sound like I didn't like the games at all (I did), but since this is what the thread is about, here it goes:
Mega Evolutions - Completely unnecessary concept and gimmick. It breaks the balance of the whole thing. Makes an already easy game even easier, and worse, it's reserved to only some (fan favorite) Pokémon that are not even native to the region... They should have wasted their time and money creating new Pokémon. Or more importantly, fixing the problems I'll name below.
Team Flare - It's one thing to have antagonists that are not that serious, another thing entirely is to give then an hollow goal. And Team Flare has the latter, which makes them a group of nonsensical nuisances, instead of a problem I'm looking forward to take care of.
Friends - Too many, useless and forgettable. And that's including the rival which is not a rival at all. I know the games are targeted towards kids, but the whole "Maybe The Real Achievement Was the Friends We Made Along the Way" that's shoved in most modern kid stories, XY included, is something that sounds good on the surface but is a bad message with dangerous consequences. Kids want to be challenged, they want to fail, learn and grow. Timeless works, entertainment works that appeal to everyone and stick from generation to generation have those elements. The "everybody is a winner" mentality is unappealing and forgettable. And that's the gibberish these NPCs repeat ad nauseum.
Gifts - I'm a Kanto fan. I started with Red back in 1999. I don't mind the so-called "Kanto pandering". I welcome it, when it's done right. Being given things away without earning them is not right. Getting the Kanto starters, which are special Pokémon, so easily and so early in the adventure is a "cheat". And these are some of my favorite Pokémon. Lucario is another example, even though it's a Pokémon I don't like or even care about. Turns out I don't even need to have to look for a rare Pokémon with mega evolution. They are given away so easily.
Story - Pokémon games, at least those that I've played, always had a simple story. I'm not asking for a complex story, but if you're going to put a bunch of story elements, they are better not be left dangling or come out as forgotten and underdeveloped. That AZ side-story felt like it came out of nowhere and never had a proper pay off. It's like starting a movie on the third act. There's no build up. Why should I care about it at all?