I quite enjoyed most of the stories in Seasons 1 and 2, but I felt that the story quality declined in Seasons 3 and 4. On one hand, it was cool that they tried to "mature" the story by making it more science fiction and making the Transformers' adventures span across space and not just on Earth. Oh, and it was the future.

And it was a good idea to change the leaders too. But it suffered too much from, "Good idea in concept, didn't work out so well in practice." Problems included:
+ Rodimus Prime worrying too much about not being Optimus Prime. No, you're not Optimus. Accept it and move on. Because he didn't, it really held back his potential as Autobot leader.
+ Galvatron just sucked... sure, G1 comic Galvatron was crazy too, but he was demigod powerful kickass crazy, whereas G1 cartoon Galvatron was embarrassingly crazy... like that relative you never want to invite to your wedding.
+ WHY were the Dinobots suddenly kid-tarded?!? Sure, they were never Rhodes scholars to begin with, but they weren't
infantile tard monkeys either! In Seasons 1 and 2, the Dinobots just traipsed around kicking butt... in Season 3 most the Dinobots were pretty lazy, and Grimlock just went about being clumsy and stuff. Oh how the mighty have fallen.
+ Wheelie. If Grimlock wasn't Jar Jar enough, they gave us Wheelie. The high pitched voice and rhyming is one thing, but the fact that he and Daniel just wasted SO much screen time and contributed so LITTLE to the actual plot of the story was just stupid. The exact same complaints that Star Wars fans made about Jar Jar Binks in The Phantom Menace... little wonder that Wheelie, Daniel and Jar Jar are often compared. Hey, at least Jar Jar helped make the Empire... don't see Wheelie doing that.
"Who the f$% is this Autobot?!" - The Rude Awakening of Optimus Prime
+ Wheelie and Daniel's time wasting meant that a lot of other toys got less screen time... how about giving us more action from Tailgate, Swerve, Pipes or HUBCAP!! Hubcap's a WAY better toy than Wheelie (who's easily the crappiest of all the G1 mini Autobots) and yet he got ZERO screen time!