Pikachu evolution family (including Pichu and Raichu) were not in Unova Dex, B2W2 did not make Zangoose and Seviper version exclusives, version-exclusive key systems, no 3rd versions.
B2W2 had a good plot imo, so personally I don't have problems there. But I'm also one of those that was disappointed with the Easy/Challenge mode being unlocked post-story. And that the main character from the Memory Link data could have helped an appearance. Really, if the Memory Link can activate certain battles (Bianca and Cheren battles), having Hilbert/Hilda make an appearance would have been neat.
Another small disappointment is the lack of information provided about the B/W characters in the Join Avenue. The 'if they have a record in Hall of Fame' and all that. It would have been neat to have that information displayed for BW characters that own shops in the Join Avenue.
I kind of wish that the two Shiny Pokemon (Dratini and Gible) Would be randomly choosed, I have Pokemon B2 and I really want shiny Dratini! :saiyan:=Pure rage! Lolz
For me, mainly the fact it felt like a rehash of BW1, which I found to be too easy/linear, and the fact they decided to make it on the aging DS, even though the 3ds is already out and making a new game on the 3ds would push tons of consoles.