As I rewatched Season 3 to prep for Season 4, several things stood out to me. (Notice I said me - not speaking for anyone else and their experience.)
1) While the season seemed uneven, I was able to pick up on the general story thread that was building. My example - the episode where Shaw stated the Ring was trying to convert an agent. We later find out that the agent targeted was Shaw.
2) The fact that were was a story thread building. Season 1 - shortened due to the strike - seemed a collection of episodes. Season 2 - attempts at an overall thread but still had an episodic feel to it. Season 3 seemed to be their attempt to tell story of the course of the season.
3) Some of the things I nit-picked on the first time around were smoothed over during the re-watch. While a few things bugged me (uneven and not very well explained love interests), others made more sense to me when seeing the whole picture, like Shaw and the whole Ring arc.
While Season 3 isn't top of my list for a favorite season, it was a decent season in hind-sight. I probably didn't give it enough credit the first time around.