I found that season4 started strange, didn't feel like the Alias we knew, mainly because of the "reset"... new location, new setup etc. and the stories were not obviously connected. But as the season progressed their were some story threads that begun to emerge, like the mysterious person that Jack and Sloan are looking for, or the "other" Mr. Sloane, Nadia's backstory, Jack's illness etc. and then the 3 part finale was fantastic.
I thought one of the problems with the show was that each time it rebooted itself, it stayed essentially the same. That season four rolled around and the CIA actually had a division run by Sloane was painfully, idiotically absurd. And far too many episodes started to use the "we need to grab this piece of technology and sabotage it/place a tracker on it" plot.