The special stat, obviously, but for things that other people haven't mentioned, there's the fact that so many pokemon were poison type. Unforgettable HM's were stupid too and were obviously something that would get changed in future editions, but not especially wierd.
http://adamgaming.blogspot.com/ - My game review/design blog, which I have finally gotten back to updating. Sporadically. Jesus saves. PSN: Orethen