If there's one thing I'd very much like to see in this game, it's missions that play out the way a series episode might. Where instead of simply running from waypoint to waypoint, ticking off items from the objectives list, a player must really explore the environment and figure out for themselves how to solve a situation given the resources provided.
Interplay's 1993 game Star Trek: 25th Anniversary managed this quite nicely. Sure, it's a rather different interface to STO but the premise is there. It is possible to accomplish.