What I would like, if not in Diamond and Pearl so much as any future Pokemon games, is games with two completely different storylines, similar to The Legend of Zelda: Oracle of Ages and Oracle of Seasons. There has been a trend in Pokemon games as time has gone on:
Red/Blue Differences: Obtainable Pokemon
Gold/Silver Differences: Sprites, Pokedex data, legends
Ruby/Sapphire Differences: Pokedex data, legends, slight storyline changes
Now, I'm not saying this will be in Diamond and Pearl (it most definitely won't, actually), but that doesn't stop my saying that it is a great idea -- after all, a great many non-Pokemon games complain about the sheer number of games compared to storylines that the Pokemon series has. (For the portable RPGs, there are three storylines for twelve games. That's seriously wrong.)
The Legend of Zelda: Oracle of Ages and Oracle of Seasons each received a 10.0 from IGN. The reviewer noted that one of the reasons he gave such a high score was his surprise that the games were so different and yet had such perfect connectivity. I say Pokemon should take a leaf out of Capcom's book.