A. They're too strong and thus ruin the challenge of the game. B. They're too hard to catch (catch rate) and I don't really care to deal with that hassle.
Pokemon can be challenging?
Challenge Mode was decently harder if you used a full team, but not really. And HGSS is hard because of the horrible leveling curve that results in you being way underleveled for the Gyms if you don't grind.
Official Meta Knight with his Brobat http://i.imgur.com/WvefuGH.jpg?1