Lately I've been switching between bouts of STO and Dragon Age Origins by Bioware. It struck me that the tactics control system used by DAO to direct party members would be perfect for STO.
Think of how useful it would be to have a system in which a "check for condition/implement action" rule is set. A list of options for each individual BO would control whether they are aggressive, passive, guard other BOs, flee melee attacks, keep a set distance from Borg drones or use certain items at certain times... just to name a few of the many possibilities.
I realize that STO does this to some extent, for instance my science BO's will heal me when needed (sometimes), but there is a lack of fine control over abilities in the chaos of combat. It would be nice to be able to set conditions in which, say, your medic would heal you only if you are below a certain amount of health or your party would not attack enemies in stasis fields in order to maximize stasis time.
Don't get me wrong, I'm not suggesting that Cryptic should duplicate Bioware's system exactly as it is (obviously copyrights would be a factor), but having finer control on the ground would be helpful in making that aspect of the game much more entertaining.
Lastly, being able to take direct control of a BO would be an excellent feature. Your primary character would switch over to a pre-set system of tactics and condition/action tables while not under your direct control.
Hopefully the aforementioned condition/action system is something being kicked around the meeting rooms in preparation for Season 4. If not, I believe it is something players would enjoy and merits examination.