First, because several people in the beginning of this thread brought it up, Pineco and Forretress are Bug-type because they are based on bagworms. Grass-type on them would make no sense.
Also, Gyrados and Charizard are not Dragon-type because they would have been far too overpowered, especially in Generation I. Think of how many trainers would have chosen Charmander just so their rival couldn't have it. Not to mention how common Magikarp is and the low level at which it evolves...
I agree, however, that Vibrava/Flygon should have been Dragon/Bug.
In my opinion, Ninetales should have become Fire/Dark in Gen II, due to its vengeful nature.
The Gothita line would have been more interesting as Psychic/Dark, and I thought Reuniclus should have been Water/Psychic (assuming it's based on a cell). Oh well.
I will probably have other thoughts on the matter. But for now, this will do.
EDIT:
I wish Seviper had been Dark. Design-wise, it's one of my favorites, but the pure Poison typing makes it less to my strategic liking.
I've always thought Serperior should have been Grass/Dragon. This would increase its movepool without overpowering the 'mon. It would have 4x weakness to Ice and remain weak to Dragon, Flying, and Poison while the Dragon type would make it neutral toward Fire.