Alrighty, I've put in a good handful of hours head-start and post-launch and here are some thoughts to make gameplay more interesting. Apologies if any of this is in there, but too advanced for me to have found yet ;-)
1) Design your own torpedo spreads: configure range, yield and spread geometry in a torpedo spread sub-menu. "Computer tactical program Worf Gamma II"
2) The picard maneuver - in an engagement an attacking ship fires, warps across the field of battle to a flanking position (or closes the distance to the enemy ship), and then fires again immediately after dropping out of warp, giving the illusion of being in two places at once
3) Cybernetic "elite" level bridge officers or one-off allies for special campaigns (surely by the 2400's Data and/or Lore have descendents)
4) I might have missed some resource material in the manual and tutorial since I was in a big hurry to get playing, but some user-configurable tactical commands would help with rallying teams in fleet actions (e.g. task group formations, designate a primary and a wingman, match course AND speed, defend/patrol a user-configurable ellipse, auto-engage attacks like a strafing run or run circles around the bigger/slower capital ships, rank opponents in a melee or fleet battle so if a teamate destroys your primary target there's a protocol for what becomes the secondary and subsequent targets - such as distance, line of sight, threat level, damage, etc.)
5) Finally, and maybe most glaringly absent, in the TNG and Voyager era the computer was like an omniscient omnipresent narrator. Obviously that level of AI and database architecture doesn't exist but an enhanced ship's computer option would be great, especially with a collection of multiple-choice voice commands that are either mission or location specific.
Also, I get the mechanics of leaving a planet or base, exiting to the system, then exiting to the sector, then crossing into another sector, then reversing the steps to get into another action or mission, but it would be handy if you had the option to "automate" the voyage, i.e. I accept a mission from Commander Sulu and then a handy graphic cuts away from me beaming out and fades into my ship coming out of warp into the system in question. I think cross-referencing the systems with the sectors on the maps is a little cumbersome, and some of the mission assignments don't mention the specifics needed to get from starbase to away team. This leaves opportunities for randomly generated "deep space encounters" en route - how many times does an episode begin with the ship shuddering, the yellow alert claxon sounding and the duty officer asking "why did we just drop out of warp????"
And on a final note, isn't it ironic that the in-game economic system (micro-transactions, energy/skill credits, merits, etc.) is so complicated when the Star Trek universe of the the shows and films featured an essentially currency-free society?!?
I'll think of a witty signature later - gotta get back to the crystalline entity!