While writing my episodes, I was think "It would be good if..."
1) Designate professions with costumes when applying them to NPC battle groups. So if you place 2 science officers in a group, they aren't laying down generators and holding assault riffles.
2) Apply costumes to away team/ player ship. I have a section where you portray another character, so you are being called by the other characters name, but you still look like you. would be nice to look like the character being portrayed in this case.
3) be able to trigger a NPC contacts off like you can objects. Same with friendly NPC fighting groups.
4) make the social ship interiors accessable in foundry. the only federation engineering room is on a red alert damaged interior. Id like to simulate the ship being boarded on the ship interiors we actually can use on our ships.
4b) Make captain ready rooms on bridges enterable. they are blocked off from being entered.
4c) Conference rooms. Could be added to black spots of already produced maps.
4d) Shuttle interriors.
5) Non-mission critical map teleports/turpolifts. Pretty much a map-transfer option under special that doesn't trip the story. Good for making turbolift go-arounds for blockades on the same map without having to duplicate maps.
6) i've looked but haven't seen real forks based on A-B outcomes or players specifics, like being a tactical officer or engineering officer.
7) Timers. Can go along with 6. If you do something in set time, you go along A path, but B path if you don't.
8) Forced shuttle. Some missions are meant for shuttles.
9) Solo away teams. Have option to allow "players" or not whena active.
Since you have a post up -- I hope you don't mind me adding to the list here.
1. Single NPC placement... not squads. This way we can create and compose a fleet/squad the way we want altogether. I wanted to put together a Fleet for a fight and was dismayed that all I can do is put a costume on a ship, say a cruiser. But that "cruiser" is a costume that may appear over an escort, SV, or an actual cruiser (of very likely different class/type).
2. Ability to make NPC contacts WITH combat triggers. IE an ally that you can hail, then you get ambushed, and won't just sit there like: "Oh, they're fighting... what should we do?" LOL. Or the opposite, so that if you choose a specific fork in the conversation, it ends up stirring a fight (and maybe failure hint, hint). -- similar to what the OP posted in a way.
3. Make contacts so they can be hidden after dialogue. IE I wanted a ship to rendezvous with the player (via warp-in <BUGGED>) talk to the player, then warp-out after the conversation is over...
4. Need more ship interiors or objects to make proper maps in addition to exterior custom maps being possible. I searched and searched for a Fed interior with a Warp Core, the USS Warwick was the only one and it bugged on my first attempt to create that map. (Did get it working though).
5. Making a combative target part of success/failure. I wanted the fleet in No. 1 to have a ship that had to survive an encounter... then I thought it'd be cool if the number of alive ships at the end would end up being greater reward/assistance later. IE scenario as before only the ships that survive can be summoned at a battle later or be a trigger for events unfolding later -- similar with what OP suggested.