I'll say this: it still has, to me, the single best fight between Optimus and Megatron in the entire franchise.
Admittedly, when I saw it as a kid, I didn't really watch all that much of G1, so the deaths of the characters didn't affect me that much, even Optimus, who's one major scene is just so awesome.
Now, the weird thing is, I saw it years later and hated it. But for whatever reason, I saw it again a few years after that and it became my favorite animated action movie ever. I just love all the set pieces, the dynamic transformations, the soundtrack. Even Daniel and Wheelie didn't bother me that much. Though even as a kid, Hot Rod was more my perspective character than Daniel.
I guess that's the thing about it compared to the Bay films for me: the Bay films are more or less standard alien invasion films with the twist that some of the aliens are heroes. This...I honestly can't think of anything like it.
Though I really, really love Animated, too.