1. I might just be too lazy to want to press Y again, but I hate how they force you off your bike in the little transition buildings between routes or routes and cities. It just bothers me, especially since I end up hearing the biking theme much more than necessary.
2. The wild pokemon encounter rates are indeed annoying. Enough said.
3. I was kind of turned off by the lack of variety in the Pokemon you can use while you're trying to go through the gyms and the Elite Four. For a type "balanced" team, almost everyone seems to have a Luxray and Alakazam (or rather, "Kazza"). Not to mention the utter lack of fire types.
4. It's kind of hard to describe the feeling, but a lot of the towns and cities seem lacking. They're a lot more aesthetically pleasing, yes, but there just seems less in the towns/cities to explore, and less interesting people to talk to. For instance, the cathedral-like building in Hearthome... I was really expecting it to have some significance, and Celestic Town was more or less pointless.
5. Probably my biggest complaint- I don't really like the design for most of the new Pokemon. In my opinion, they look a lot more like actual monsters than animal-like creatures, and a lot of them are just further evolutions of older Pokemon. The general cuteness and creativity seems to have gone downhill.
6. Way too many legendaries. And I wish they would go back to having Fire/Electric/Water (or Ice) for the trio legendaries.
7. Not so much a complaint, but I have the hardest time taking Team Galactic seriously. Not that I've ever taken any of the antagonists seriously, but I just can't help but snicker whenever I battle them. They look like characters from a bad sci-fi movie, and what's with the bowl cuts for the grunts? On a similar note, I wanted to shove my head under a pillow and cry when that one fisherman said "for the win" and when that little kid said "people treat you like a noob."
I have plenty more complaints but that's all... for now, heh.