My main issue with Clone Wars filler was that so much of it just took the form of "battle on planet X to save it from the separatists". I didn't mind that the episodes were self-contained stories (a lot of the more creative ones were really fantastic), but a lot of them felt like they were retreading the same ground over and over, especially in the cases where they stretched out a one-episode premise for an hour to fill up the season quota.
Having said that, I think it's just one of the ways in which the show was bogged down by the source material and overall premise. There was less room to have original, fun, star-warsy adventure episodes because the whole thing had to be rooted in clones vs droids. That's why I'm more hyped about Rebels, since I can see it having the freedom to do more with the source material than its predecessor.
And the main issues with the prequels aren't generally to do with acting or annoying alien characters, although they're certainly easy targets. I'd probably argue that, overall, the prequels might well have a more talented cast than the classic trilogy. The problem is that the scripts they had to work with were so atrociously bad in every aspect, from the characters to the dialogue, from the plot to the pacing. When you add bad direction and editing on top of that and factor in an inappropriate reliance on CGI, the prequels fall miles behind the original trilogy (although explicitly episodes four and five) in terms of their overall quality.