Beast Wars is so infinitely superior it's difficult to compare them.
I enjoyed the First Season of Beast Machines though, but the show went horribly sideways after that. The idea of a Megatron who'd "won" is always a good storyline to explore, and the show did a fair job handling and expanding a lot of Transformers lore, even if some of that lore expanded into "we need to make peace with organics" bullshit.