I think the problem Prime had was not that it was too short, but that it was too padded. Darkness Rising was awesome, no denying that. But it seemed to fizzle out after the second season. Prime tried to be mature and epic, but it was too ambitious in it's attempt to flesh out Cybertron's history with the Relic Hunt. Trust me, the same thing happened in Beast Wars [namely in Season 3] and to an extent in Animated. And judging by how Hasbro is giving a big push to promote Beast Hunters as the final season, maybe it's a sign that things are improving.