I having just finished Beast Machines I can see how it pissed off so many:
Nightscream (*shudder*)
Megatron's sudden anti-beast mode agenda (I swear he used to love his beast modes, especially the dragon...)
Cranky pants Silverbolt
I can also see how the ending rubbed a few the wrong way...

oh and of course the whole techno-organic angle.

I'll get this out of the way (light the torches and get out those pitchforks!) I like the techno-organic stuff, it seemed a logical evolution of the beast modes
.
1. Basic, organic beast mode, 100% robot on the inside, then
2. Transmetal, robotic beast mode, more organic bot mode, then
3. Transmetal 2, organic and robotic influence on both modes, and finally
4. Beast Machines techno-organic bot and beasts.

hell even pretenders (G1) seem to foreshadow the organic end to some extent. (In the IDW-verse anyway)

The show had its issues, pacing, the always on the run stuff can get boring, and the new cast were mostly lacking in character, Vehicons boring... untill Rhinox came back, sure he came back evil, but as if he wasn't already! He made on hell of a predacon! and explosive fart attacks are against the rules of war!

the biggest design flaw was that the beast modes and the bot modes didn't even look like they transformed into each other and the toys suffered massively due to that.

but there was some good that came out of it, Savage/Noble was an interesting concept, being a 100% organic transformer. It also cements BW Megatron as the greatest villain in the Transformers G1 continuity family, he enslaves the whole of cybertron! If that don't get you bad-ass points nothing will!

Overall not the greatest series, nothing on the G1 or Beast Wars series, but a mostly satisfying conclusion to the G1 continuity family.