Slightly less of a problem when you train something that evolves at an obscenely high level anyway. (hugs Ulgamoth)
I had several issues, mostly re: certain typings. The starters, for example. Pure grass, pure water and FIRE FIGHTING AGAIN ARGH. Daikenki had great potential for being Water/Fighting, but never got it. Another thing that should have happened and didn't re:types is Wargle. That thing would have made a perfect Fighting/Flying, a type combination that I personally would have loved to see - and it would have worked so well with its version counterpart being Dark/Flying. Would have required a minor change in its learnset to be really effective, though - I mean, would it have been so hard to shunt out useless shit like Defog and Whirlwind for, say, Close Combat and Seismic Toss, or the ability to learn Brick Break? The fact it is male only while Vultina is female only is also nine kinds of stupid, at least. And speaking of types, we had some pretty interesting typing potential windows that were blatantly missed: the Gothlolifail line could have made an interesting Psychic/Dark, for instance, rather than another pointless pure psychic.
The TM distribution in this game also borders on fucking ridiculous. The actually useful moves you can only get past the point in which they would be particularly useful to you. The fact they're continuously reusable is a nice touch, but that's about fuck-all useful if they aren't accessible, and sadly, they fucking aren't - especially when some PokeMon (such as, say, Choroneko/Lepardas) have godawful learnsets which relegate them to pretty-lawnmowers-and-little-else status pretty damn quicky. Also would it have killed them to give Gobit/Gorug the elemental punches or indeed anything else that could benefit from their potential Iron Fist ability? Such a waste of potential. Siiiiiiiiiigh.
Also, the important NPC cast in this game are certainly the weakest design-wise the series ever had, even if some of them make up for it with unintentional (or sometimes intentional) hillariousness and/or badassitude. The lack of gym re-challenges also saddens me (Aloe needs her fucking Buffalon. Seriously.) although, come to think of it, the first two versions of a generation NEVER have gym re-challenges, and the feature is always added in the third version, so we'll obviously see those in Gray (or whatever they'll name the third version of Generation V).
Otherwise, as ever, certain PokeMon are way too late-game to be practical (I am looking at YOU, Kuitaran! X_X) and the new EXP distribution system renders level-grinding even more annoying at times (which can be a huge damn nightmare if you're trying to raise a PokeMon that takes a while to reach its true potential, such as Merarva/Ulgamoth or godforbit Monose/Jihead/Sazandra - although the free Lucky Egg certainly helps!). Some animations for gen 1-4 PokeMon are utterly fucking terrible (YES, MAGMAR, STOP FLAILING YOUR ARMS LIKE A RETARD PLEASE).
Also, I am seriously waiting for an explanation re: Kyurem. Seriously. What are we betting this thing gets a new forme or two come the third version, having to do with the its two hidden signature moves, Cold Flare and Freeze Bolt (which appear to be linked to Reshiram's Blue Fire and Zekrom's Lightning Strike)?
Yeah. I have my fair share of complaints and grievances, but Gen V is still for the most part quiiiiiiiiiiite awesome ^^