Sarcastic humor aside, the single thing I dislike about Joss is the thick plots. If the plot is so thick you have to explain the entire season episode by episode to a newcomer, then something is wrong. TV shows should work to keep everyone up to date on the latest happenings and what has happened. If they fail to do that effectively, then you're just catering to your current viewers.
Example: Angel. This is, I admit, the only Joss Whedon I watched all the way through besides Firefly. But I did skip a ton of episodes. Why? The plot was too thick and each episode didn't really solve anything -- they usually made their situation worse. Finally, it got to the point where I skipped a bunch of episodes (I missed Faith's return, apparently). Then I think I skipped some more until Jasmine came along. I figured that was a good restarting point. But even then, the plot was uber-thick. I very much liked Season 5 when Angel's gang runs the new Wolfgram and Hart. It was episodic, it was nice. You could tell the budget was limited because they barely went anywhere other than the office building, but I still liked it.
And now I'm getting sad because Dollhouse seems to be following that same trend. I still <3>
This has been an early morning rant by yours truly.