Beast Wars is not without its flaws, especially early on and the animation has not aged so well in some respect. I do feel the character models are very good (especially season 2 onward), but its the environment and lighting. Dear god, that season 1 flat texture grass and lack of shadows! Its painful to look at nowadays!
It also had flaws in its narrative and some plot points went nowhere or were poorly handled. I will admit those are valid flaws. But its wrting was good (and still is), its voice acting was equally great. Sure, it had flaws but it was a major step up from Generation 1. In a way, BW is to Transformers what Next Generation is to the original serie. Or what Zeta Gundam is to Mobile Suit Gundam.
Beast Machine is (pardon the pun) a whole different beast. However, its deepest flaw is that is completely butcher the characterization of characters we came to know and like in Beast Wars. And that is a more serious offense, in my eyes, than its different take of Transformers. Because it hurt BM. Whereas being different merely enhance and makes it a truly unique installment in an otherwise sometimes predictable franchise. It was also, at the time, the most story-driven cartoon on the air.