This change would allow for expansions to be a somewhat separate game involving fleet controls and other "admiral-level" abilities. It would also stay truer to canon, in that Captains are the driving force pervading the universe (i.e. the most common ship commanders).
We would also need to re-do the tutorial slightly, but doing the tutorial as a cadet would make more sense (to me at least), and would give new players a fitting introduction. Successful completion of the tutorial would place new players into the role of Ensign, a fitting place for new characters to start.
These changes, coupled with the idea of tier elimination and a new Tutorial, would make STO much more "Star Trek", while still retaining the current STO feel.