What they messed up with in Diamond/Pearl is simple.
1) Too large a Pokedex. Collecting all 450+ from every past game is mind-bogglingly immense, and I don't see a lot of people actually pulling it off.
2) Too many past pokemon. With all the new pokemon available, why bother catching Geodude or Zubat yet AGAIN, even if they are reliable? For each new Pokemon game, they shouldn't use anything from a game older than two games old (i.e. in Diamon/Pearl, don't use anything from Red/Blue).
Some genius moments in Gold/Silver/Crystal are looking unfortunately overlooked, like the traveling to Kanto region. I loved that part, and if you could do it all over again (or even better, CHOOSE which region you want to start in), then it would be amazing.
And finally, expand on available starters. For instance, I love Beldum, and would LOVE to go through a game with him as my Starter type. The experience would be a lot more personal. (Obviously, this plan would require a lot of Red Tape, but it could be feasible).
To sum up, if they could make the entire Pokemon experience a lot more Personal, it would be very impressive.