Lack of a good solid outline.

Even though Episode 1 is my least favorite of the prequels, that particular film still feels like a lot of planing went into it. 2 and three on the other hand feel really choppy and uneven, like they were rushed to completion. Much like a lot of the crap that came out around the writers strike.

I think if Lucas had put together a much more clear idea of what was going into each movie from the outset and really fleshed those ideas out rather than going into production with scripts that weren't even finished, then they would have played out much more smoothly.

I do like that they are basically using the Clone Wars to address some of these story telling issues with the movies but they shouldn't have to.