There was plenty I liked about season 3, including Rodimus. He was badass, sarcastic, fearless, decisive; everything you'd want in a leader. Granted, the writers focused on his insecurities far more than was necessary. But overall, dude effin ruled.
Blitzwing was becoming an awesome character, having to choose between allegiance and his conscience. Too bad he was dropped from the show.
Post movie, the show became alot more sci-fi, expanding across galaxies, dimensions, and time. It also had a darker, grittier feel to it, which especially appealed to me.
And although there were some stinkers (Nijika, Carnage), there were also a handful of outstanding episodes to offset them (Awakening, Webworld, Burden, Human, Primatives).