I didn't like that a lot of pokemon seemed too similar to the old ones - Like Boufallant, Foongus and Palpitoad family's. Although in saying most are ok, and a few are amoung my favorites.
This was made worse by not letting me have any older pokemon to use while I got used to the new ones. (rightly fixed in the sequels).
I didn't like the musicals, but I do give them credit for doing something different rather than just more contests. (even though I liked contests, especially Hoenn's)
Fire/Fighting. Really just stop with it.
That Antique shop in Join Lane - always, everything was a hard stone.
I did like the much stronger story-line, and the use of sequels rather than the third version, however I would have preferred a third version that was a sequel to both at once. (Yes I know that wasn't possible with the story, but maybe for the future).
I liked the much more animated sprites.
Join Lane in general, and Nurseries in particular were great, so was Volcarona's egg speeding ability (forgot the name)
I actually liked the Films, although some were rather tedious and I still haven't finished a lot of them.
Dream Radar was nice, although I don't want it repeated... unless it's built in or free.
I don't use dream world very often, but it was a nice alternate way to get unavailable pokemon, and I look forward to (hopefully) seeing a better equivalent in gen VI
I liked Yancey, nice to have some level of a relationship with a character other than the prof. and your friend/rival.
I like the bonus custom PC backgrounds, hopefully there will be more in Gen6.
I liked that your rival (in the sequals) has a purpose other than trying to be as better than you are.
I like the extransevers screens, but wish they had made sprites for the gym leaders, random trainers so we could have rematches and hear about top percentage Patrat
Pokemon world tornamant was one of their best ideas yet, remiked Hoenn music was amazing - only two complaints with PWT. SABRINA. I could beat any of the other kanto leaders, but not Sabrina (she didn't even have a type advantage). After about 30 attempts she lost to Janine in the semi-finals. I was actually at a type disadvantage to her, but still won. Secondly WTF WHY IS FLANNERY NOT A PROPER RED-HAED. THERE ARE ENOUGH PINK HAIRED GYM LEADER ALREADY. (as you may have guessed she is my favorite gym leader, and if/when Ruby/Sapphire is remade she had better not have pink hair... you have been warned Game Freak)