It seemed to me that Dollhouse was set up for a 5 year arc.
Year 1 was been about Echo becoming 'self-aware' of herself, which happened at the end of the season.
Year 2 was been the Dollhouse War that we see, conflict between two or more houses and uncovering a bit more of Rossum's agenda, as well as finding out a little bit more about Caroline and the others before they were dolls.
The last 3 seasons (of 12/13- I'm not sure Dollhouse would've suited a 22 episode run without a lot of fillers a la S1, it needed that sense of 'condensced intricacy you get over a smaller number of eps.) would've been Echo out in the wider world, on the run before deciding to come back into the Dollhouse to take them down from the inside, also Echo learning to control her 'gestalt' powers while she finds out more about Rossum's scope/future plans, plus her romance with Ballad,
Siera and Victor developing into loving on another, Topher gaining a conscience as Rossum uses his genius to develop their 'programming' technology, Adele losing control and then regaining control of her own house should've taken place over a season.
Hell, the last season coul've been set in the post-apocalytic world we saw in Epitaph- yhere was tons of material to work with in season 2.