as the revamp of the crew comes along, its time to make everything not revolve around your captain. watch any episode of star trek, there's subplots all the time for the rest of the cast. the Q&A about the future of the game got me thinking, and post season 4, i'd like to see missions like this, or a foundry advanced enough for anyone to make a mission like this.
a fleet of ships could be fighting the borg in orbit of an impotent federation member planet. ending with most of the fleet destroyed and you sustaining heavy damage. after the battle ends, your crew on the bridge reads off damage reports. your captain gives orders to set course to a star-base for repairs and retires to the ready room.
you then take control of the chief engineer and you do some repair mini games and direct repair crews. if you paid atention to the damage reports on the bridge, and direct repairs most efficiently, you get an acolade, merits, emblems, whatever. then you have problems contacting repair crews...
then it might jump to a junior officers in the lounge talking about the battle with other junior officers. you can conduct the conversation pessimistically, optimistically, logically, or any combination of that. your answers might have some effect on events later on...
then maybe your science officer is on the bridge running diagnostics on internal sensors and trying to bring systems back on line. the better you do here, the better shape your ship will be in when... the undine attack!
another grueling space battle, your health is caped by how well you did the science and engineering mini games. if you did a crappy job, you are caped at 75% health and cant use abilities Ltcom and up. after you defeat them, the barley functional internal sensors detect boarding parties!
now you control that junior officer again, on a security team. the performance of the security team is affected by the conversation you had earlier. the undine seem be intent on reaching deep engineering levels on the ship and causing damage that would destroy the ship. a mini game might come next were doing something wrong could detonate an eps conduit and cause a hull breach that kills that junior officer and his team.
after the undine are defeated, the senior staff meet and discuses the apparently suicidal undine, stating that in the past they are more intent on capturing ships and replacing its crew, not destroying them once boarded. here you can decide whether to continue the long safe way to spacedock through a nebula, or keep heading strait toward it through unsafe space. this could effect something, i don't know.
later you chief engineer gets cornered by borg in a jeferies tube! (thats why the undine were trying to destroy the ship, its infected with borg!) you fight your way out as him, but don't get nano probed! maybe he gets assimilated and you can rescue him later, or kill him. or he escapes and gives you an early warning making the next fight easier.
lets say your junior officer screwed up and there's that hole in your ship, release the force field and suck out a bunch of borg, and crew, to make the fight against them easier. (at the end of mission you might get court marshaled for doing this) if there's not a hole in your ship, maybe security force fields work and you can lure borg into sections and trap them, and in those sections you can beam them into space. otherwise fighting them would be extremely hard without choosing one of these options.
maybe the borg at this point activate your ships transwarp and your taken deep into gamma orionis. your captain contacts the bridge and finds they still have control of conventional warp, and he orders you head for the transwarp conduit and fleet there. at this point you fly through sector space getting chased by borg ships, if they catch you you might have to fight off a sphere or something.
when you reach the fleet who ever is on the bridge contacts the fleet and you have another conversation mini game. screw it up and the klingons destroy your ship, screw it up not as bad and survivors are beamed off and your ship is destroyed, do a fair job and the fleet gives you space and fights off any borg ships still chasing you, but you have to deal with the borg on your ship without support. do good and an army of starfleet security npc's beams to your ship and you can sit back and watch all the npcs slug it out wile your captain makes a surgical strike at the main borg node thing, making them disoriented and rout able. do the conversation perfect and a bunch of klingons beam over to help too. at this point, the mission FINALLY ends.
this is the potential the game has. i hope your 1 playable captain character becomes your whole group of officers and ship, just like what the shows were about. it was always about the whole command staff, not just the captain.
your captain cant be everywhere at once, stuff is going on all over the ship that hes not a part of. control different officers at different stages of missions!