I'm fanboy enough to consider this a 10/10 in spite of its flaws and the clear best since R/B/Y/FR/LG (none of that going back and forth between the same 3-4 towns for five hours from G/S/C, for example, none of the stupidly massive expanses of ocean from R/S/E), but nonetheless...
-Still no option to have all text appear at once instead of scrolling. The fast option isn't fast enough.
-Still no option to have the health bars drop immediately. Or even just by percentage instead of the hard number. Getting rid of Blissey, Drifblim, etc. takes too long to watch.
-Encounter rate doesn't seem higher to me, but that's irrelevant because even the Advance games were too much. There's never a time where I don't have 25+ Super Repels on me. (Super Repels being a lot cheaper than Max Repels, and only lasting 50 steps less.)
-Surfing is too slow.
-Level 1 Pokemon are not a problem to me. Level 1 Pokemon and no Emerald breeder, though, that kind of sucks. Usually I just slap some Exp. Shares on and head to Route 213 to fight the Tuber kid and his three level 51-53 Gastrodons, but I shouldn't have to. I have 353 Rare Candies, earned legit via Pick Up and 13 runs through the combined GBA/DS games. Let me use multiples in one shot.
-I'm torn on the convention change for capitalization. On the one hand, items, moves, trainer names, Pokemon nicknames, etc. look nicer with normal capitalization. On the other, even if it wasn't necessarily pretty before, at least it was consistent before--and now it isn't. Everything has normal capitalization except the Pokemon names. I'm taking a maybe not-so-wild guess that those are still all-caps because they were copyrighted that way, but still. And besides the Pokemon names, the menus are also in all caps, the Pal Pad looks especially strange since two of the options are in all caps while the third has your name done normally and then caps from there--and, well, you get the point.
-There was one thing Colosseum did very right in terms of gameplay, and that was letting you start again from the level you lost at in Mt. Battle. This needs to be implemented in the normal games' Battle Tower. The items you can win are great, but buying anything is too tedious as-is, since you're bound to lose eventually by criticals or OHKO hax or Double Team or whatever.
-R should be a second item toggle. (And L could be an option, for that matter, although I'd still keep L=A on.) The Bicycle and VS Seeker are the only two key items I usually use, and it'd be nice to never have to dip into that menu for a single item.
-Speaking of the bike, why do they make you get off of it at the checkpoint buildings between cities? Or why even have those checkpoints to begin with? If they didn't, I wouldn't have the above complaint, because I'd only need to get on my bike exactly once every time I exit a Pokemon center.
-No buying 5000 coins, even though some TMs cost upwards of 10000.
-No more PC item storage. It's annoying scrolling through a list of 55-60 hold items to get to the one I want, and the only other real option is to stick them all on Pokemon in the box and move them around that way--which is also annoying.
-Cutting Recover to 10 PP. Okay, yes, R/S/E had to be reactionary against the stalliness of G/S/C, but how far did they really have to go to nerf the idea of playing defense in D/P? Having so many more offensive items, and improving the old ones, already served that purpose...
That's about all I can think of for now. Lots of nitpicks, but eh. I tear down because I love.