I mentioned this idea in another thread, but I wanted to propose it here as well.
It seems that people love the idea of lvling though the DOFF system. The DOFF system also seems to be a really really bright spot in an otherwise hard to swallow beta best.
For me, it makes up for the lack of trekkiness in STO in a lot of ways. I am finally the captain of my ship, not just captain of my BOFFs (or simply my powers/ attack pets).
For me, I am closer to my DOFFs than my own BOFFs as they can either wind up in sickbay, die, or succeed and remain quite vaulable to me... my DOFFs also have more biography than my BOFFs do, who have zero biographical history. My BOFFs are simply powers, without traits or unique specializations.
For me, I am jealous of the missions my DOFFs go on. They are continuing everything that is Star Trek, while I am wasting my time grinding for Dilithium.
For me, I wish I was a DOFF, gradually being sent to lead missions where I explore, negotiate treaties, recruit bridge officers, collect anomalies for my captain. Eventually, I would be granted the title of Captain and be able to commission officers to the same while having the freedom to answer hails (mission givers) at my leisure.
For me, my Admiral wishes he was commanding a fleet of ships, or Command Officers- COFFs.
Simply put, I believe that ALL new mission content needs to support the DOFF system rather than stand apart from it. The DOFF system and future expansions of said system needs to become the heart of STO because it is Star Trek.