Okay I have A LOT of criticisms:
1) The battle animations where the pokemon move suck as it's really pixilated which is annoying.
2) The new pokemon are mediocre, but their names are terrible. I mean trubbish? And Thundurus? That's just thunder with an us on the end. And don't get me started on that zebra thing...
3) The story line is poor. Team plasma fail miserably in comparison to team rocket or galactic as they aren't really villains, they are just annoying hippie morons. The point is they are meant to be evil, not misguided morons who serve a child as their king. Also, seriously, the bad guy is called N? That's not a name; that's laziness. Oh yeah and how could I forget Roggenrolla? That is just horrific.
4) Cheren and Bianca. I can't stand them. I liked it better when you had a neighbour and then a rival. Cheren and Bianca were annoying.
5) The postgame is too short. HGSS has 8 more gyms to fight, and this has 3 towns and some new caves. Pretty poor considering the main story was so short to begin with!
6) The elite four were terrible. I beat them first time without any items other than 10 hyper potions and 3 revives. All my pokemon between levels 48 and 50. Also the gym leaders were rubbish.
7) No perma run is annoying.
8) The seven sages should have battled you when you found them, or at least done something interesting. Just sayin'.
9) Like in d/p and r/s the gyms and e4 should have been higher levelled. There should be more to do between gyms, so you can gain a solid 8 or 9 levels between gym battles. I miss the days when you're pokemon were level 60 at e4 fighting similarly leveled pokemon.
10) The game was way too short. There wasn't enough to do.
11) The relic items let you become insanely rich allowing you to buy anything which screws the post-game up.
12) Nitpicking now, but the gym puzzles were boring. They should be more challenging.
Okay now for things I like:
1) HMs not playing a big role. LOVE THIS, it was so annoying having to have cut, rock climb, strength, etc on your pokemon when you were trying to defeat the e4. Means you can start to make decent movesets.
2) The music is unbelievable.
3) TMs being unlimited use.
4) Variety of pokemon you can catch. Very cool that you have so much choice this time around, made the game far more interesting.
5) Decent levels on wild pokemon for a change.
Okay I'm done now