before the E4, the selection is way too limited in D/P, but then after that you access to all those new evos of the old pokemon, which is cool. My team was terrible before that though.
During the actual game, I think the goodness of the pokemon available would go something like this.
1. Kanto (good starters, and a wide variety of pokes available to mix up the team)
2. Johto (again, good starters, but the pokes early in the games were lacking, especially since I played mostly at night, all you could get were Hoot-Hoots, and Spinerac.)
3. Sinnoh (starters were kinda not so great, but you got a good flyer early on and it least there was a descent variety of types early.
4. Hoenn (worst starters, and the pokemon early were terrible, only one worth getting was Aron, and maybe Shroomish. All like 5 good pokemon in this game aren't available until way to late. These games were terrible.)