To me, Team Flare were very bland. We had this whole introduction of the Mega Evolutions, ways of bringing out a pokemon's full power and potential to levels never seen before, and although Lysandre goes on about Mega Evoluton a bit,Team Flare's plan has nothing to do with this fantastic discovery. Instead their plan was to wreck the world in some way using a legendary pokemon, only to have that plan foiled by the player character using three False Swipe attacks, a Sleep Powder and then 6-to-12 Ultra Balls, just like every other game since the Hoenn games came out. So, yeah, I found that to be dull and disappointing. About the only thing really interesting about Team Flare was that Malva was involved (and even then I struggled to give a cr*p!)
Although not a huge issue, I am a little disappointed that neither Sceptile nor Swampert have had a Mega Evolution (so far). Why should Blaziken be so special?
I really didn't like that Korrina had a Machoke. Seriously, what is this obsession with that evolutionary line? Every major fighting type specialist ever seen in game (Bruno, Chuck, Brawley, Maylene, Marshall and now Korrina) have been shown to use either Machop, Machoke or Machamp at some point. They're officially worse than rock type specialists and their Geodudes (thanks to Grant
FINALLY breaking that trend!
Some of the gym leaders were unmemorable (is that a word?) Seriously, I have to keep forgetting what Ramos and Olympia are called and I can't even recall what the last guy's name was as I write this. Seriously, the Ice guy - what the hell is his name? I'm trying to remember, but I'm drawing a blank.
I was very disappointed that the Elite Four did not get full teams after you beat them the first time. That sucked!
Lack of much in the post-game is disappointing as well, and so is the ability to go round anc challenge people rematches, either through vs seeker or registering them in your phone/device/thing.
The main rival taking forever to get a decent number of pokemon was a little annoying, and I was disappointed that Trevor, Tierno and Shauna never got full teams.
Lack of LEGENDARY POKEMON!!!
No way to get Events in GTS...yeah, just screw everyone needing good legends :/
I, for one, was actually very happy with how few legendary pokemon were found in-game. For too long thay have been trying to shove as many lengendaries down our throats as possible (both new and old). I've clocked up many hours on Y version and I've only bothered to catch Yveltal and Zygarde, both of whom are currently sitting somewhere in one of my boxes that are full of the pokemon that I don't use. Zapdos still wanders free and I have little intention of trying to track it down and Mewtwo is still in his little hidey-hole where he can stay until I decide to just go for it and try and complete the pokedex.