The missions are immersive and all, but there's one thing they really lack: consequences... What I mean is in all missions, if you make a wrong choice nothing bad happens, at max you just fail the mission... But being a captain also means facing consequences... So what I am suggesting is making missions have an influence on the crew. Ex. "Hey we need some help", and all missions always answer "yeah sure! I'll send a team of engineers over", they fix it and it all ends happily ever after. But what if it really doesn't have to be that simple? Let's say there is a warp core radiation leak on board, and the ship might be destroyed... Why not have the player decide if he wants to put his duty officers at risk to save the situation? See what I mean? I hope you'll find it to be a good idea.
What is a "wrong" choice, though? The right choice in your scenario is to beam all survivors over, not risk your crew and theirs to the skills of your engineer and their luck at fixing it in time.
Complexity makes this an issue. Even with 5 or so choices per mission, that may not cover what a player might want to do (as in my solution above). And as for consequences, that means tracking each decision for each player and spawning effects later due to some combination of choices over multiple missions.... way too complicated to implement. Immediate consequences type would work, if you mean that (save them, and one joins your crew as a BOFF or DOFF, let them die, and you get loot instead, for examples).
Yes, I mean mostly immediate consequences, it's obvious that it would take too much work to change the mission course with the decision of a player... I'm just talking about choices that wouldn't change the whole storyline.
No problem with the idea, but then DOFF acquiring needs to be cheaper and easier... though frankly with the starbase grinders running now, white DOFFs are often more expensive than green ones so maybe that'll reduce it... nah why would PWE do anything to DECREASE costs.