I love both shows, and hold them in high regards. But I just can't compare or decide which one I like more.

Toy line as a whole, I prefer Animated over Beast Wars. Don't get me wrong though, BW had some of the best engineering ever! But, there were many many toys/characters that never appeared in the show. Some of these only got "retconned" into comics/stories many years later. Animated on the other hand, is the first ever cartoon based toy line that I have a STRONG desire to collect them all, and have done so minus the repaints, which are very few compared to say the Movie line. (I do have all of the seeker repaints and Cliffjumper though, repaints that make sense to me.) Each toy just screams character. You can pretty much hear the character's voice in your head the moment you lay eyes on a toy. I'll actually go as far as saying I like Animated toys more than I like Henkei/Classics. I know it's very strange for me to say I enjoy Animated toys much more than I enjoy Henkei/Classic. QC problems aside (I haven't really experienced these myself), the only big problem is scale. The toy line would be pretty much perfect if they fix the scale.