Charizard was definitely OP in the first game—I mean c'mon, he got Heat Wave at Lv. 1 meaning he could sweep through Dungeons that would put you at Lv. 1.
Any multi-hit moves were broken, I can't count how many times Fury Attack Beedrill and Fearow beat me down in Sinister Woods and Mt. Blaze Peak, respectively.
My favorite game would certainly be Sky, as you still had a shitload of things to do, even after beating down Primal Dialga. The only problem I had with the game is that it has way too much dialogue and treats the player as if they have the memory span of a fish.