I agree with the above statements completely. But once they release the ability to introduce user-generated content, I believe this problem will VERY quickly go away. I've already had numerous ideas for how I would go about implimenting "decisions" a captain could make. This is primarily handled through dialogue chains, but the choices a commander makes makes all the difference to the mission outcome along with the ability to "fail" the mission as a means of completing it.
I have no doubt, many other players feel the same way. So, as frustrating as it is to have Ensign Jones say "Sir, the Undine have entered the system! We need to keep the Undine from destroying the planet!" Despite the fact that we just liberated our people from the Borg population infesting said planet (another plan I was throughly opposed to) and despite the fact that we just barely escaped the planet with our lives, now we're going to defend it against the Undine. When I played this mission I know I shouted, "Let them HAVE the planet!" I would like the option to say, "We've got what we came for. Helm, get us out of here!"
I know that future mission scripters will provide far more options in their dialogue chains.
A few savvy mission-makers may even include an extra mission specific crew member scripted into your away team, one that you can actually ORDER to do stuff and one that can be killed if not protected.
I'm the captain, and my decisions should have long lasting consequences.
I agree completely - this might fit in well with something similar to the way you run into Breen Patrols in Orellius Sector. You meet an alien ship (or ships) that desperately need item X: If you say Yes, you replicate trade goods and get an offering of friendship (as in Relief Effort). If you say No, you have to fight your way out.
Let's call this the "ST:Voyager" mission style, as it seems that about half of the episodes had exactly this plot.
(I'm not bashing Voyager and please don't let this comment derail the thread. Please.)
I wholeheartedly agree with the posts above. it would be great if we could feel we're actually in charge more. A simple rewrite of dialogue in current missions would help a lot, in anticipation of new missions with multiple options.