When I think about the gameplay, it's seems pretty sensible compared to Star Trek the franchise - particularly the use of "sector space", which, if you're into the physics of it all, would be necessary to prevent all these vehicles and people from crashing around in the space time continuum during their warp-speed interstellar travels. Here's my issue:
1. A ship captain doesn't stare at his ship in third person all the time (recognizing the cinematic and strategic value during battle). He should be able to walk around his entire ship and interact with his crew. Specifically in the following ways:
a. On the bridge: the captain should be able to travel and fight in space battles from the bridge, like a real Starfleet captain. Let there be an interactive hologram accessible from the bridge for the captain's use as officer of the deck / approach officer. It would simply pop you out into the third-person view we're already familiar with. This would be comparable to a submarine captain taking the bridge as approach officer at periscope depth and using the periscope.
1) Additionally, let the bridge officers be fully voiced in appropriate advisories, reports and warnings. This would add significantly to the "immersion factor".
b. Around the ship: it would be nice to repel boarders. Go to the transporter room with your away team to be transported. Visit engineering, tactical and science departments for inspection (such as to observe the installation or repair of epic gear).
c. Social: it would be great to go to your stateroom and summon your science officer for some board game, for which a player might earn bonuses of some sort. It would be interesting to be able to decorate the wardroom and or captain's quarters. It would also be interesting to have officers' parties (or captains' masts) which might improve moral and combat performance.
In each paragraph I tried to mention first the most plausible idea. Has Cryptic considered these things?