I liked the animation of Beast Wars.
The animation was good. Too bad the character design, characters, and storyline were not… :-?
Megatron definitely deserves to be number one. I mean, in the old Marvel comics Spiderman actually “fought” him; that is, Spiderman ensnared Megatron with webbing for about three seconds, due to the following awkward silence. Then Spiderman pussed out and ran away from the raging Megatron. Other than that, Megatron was nigh-Godlike.
But where the hell was Starscream? He was just as badass, too! His Armada form kicked ass with the wing sword and all. But he was classic, and he was the ultimate “stupid-but-cunning” type of villian. He died in the movie, but ah well, Unicron was there to pound everyone.