A number of story elements and character development issues were raised over the course of Dollhouse's 26-episode run. Most, but not all, had been resolved by the end of "Epitaph Two: Return". This page lists those plot points which went unresolved.
List of loose ends
The mole
Who or what is the Mole, and what is its affiliation and purpose?
Laurence Dominic
What happened to Laurence Dominic?
Alpha
Which event or series of events made Alpha turn from fierce opponent to benign aid?
Did Alpha revert to his original personality, Carl William Craft?
Clyde Randolph/Clyde 2.0
What happened to the original Clyde Randolph? How did he die? Did his body survive long enough for his original personality to be restored?
What happened to Clyde 2.0 after having been wiped from Whiskey?
Whiskey
What happened to Whiskey after the second season's finale?
What was Whiskey's original personality, prior to entering the Dollhouse?
Paul Ballard
How did Paul manage to regain the part of his self (his love for Echo) that was supposedly taken away from him by Topher in order to re-wire his brain?
Caroline Farrell
Who was the female figure mentioned in Ghost that Caroline Farrell had wanted to help?
Ivy
Did Ivy survive the apocalyptic events that occurred between The Hollow Men and Epitaph One? Did Topher convincing her to leave the Dollhouse for her own safety ironically lead to her death?
What is Ivy's surname?