Pearl. While less popular (because it's pink) Pearl has a better mix of Pokemon. Palkia (being dragon-water) is vulnerable only to Dragon type attacks and has higher speed and S.Def. Its move Dragon Rend is significantly more useful than Dialga's Roar of Time which is simply a dragon type Hyper Beam. The fossil Pokemon in Pearl is also quite a bit more useful.
Well, it almost doesn't matter which one you get. Even with version exclusives, the DS ability to trade via WiFi will make it possible to get the ones you want that are on the other game all with the exception of maybe Palkia or Dialga. It'll probably be hard to find someone willing to give up their legendary.