Well, Johto didn't have any fossils, since it was connected to Kanto... I'll put Aerodactyl there, lol.
Kanto: Kabuto, as scythes are simply awesome. Both are Water/Rock types (I think), so for me, it really just came down to aesthetic preferences. And Kabutops kicks ass.
Johto: Aerodactyl, because... see above.
Hoenn: Anorith. Scythes seem to be my weakness, lol. But I just generally like the design of Armaldo; the feathers and bug-like appearance really draw me in a lot more than the strange plant-like appearance of Cradily. Not that I don't like Cradily
Sinnoh: Rampardos, but to be honest, I didn't really like either of them. Both are equally appealing (yes, I choose most of my pokemon based on their looks; I'm strange like that
), and I don't care enough about stats to use them much. I've trained both up, but I've never used either; maybe one day I will.
Unova: I don't actually have the game yet, but I'm going to get the pre-evo of Carracosta. Why?? Water is my favorite type, blue is my favorite color, and turtles also tend to kick ass. Put all of that together, and you get my choice.