I basically had a small epiphany. The way the STO is instanced leaves for a bit of a unique opportunity.
See, one of those things that just irritates me about just about every MMO is the story. The story is always the same, your decisions (which you don't get) have no impact, nothing matters. You could completely ignore the story and it wouldn't matter.
Well STO's story is a little better than par at least, but I thought, well, its entirely possible to put decisions in because of those instances.
How it works is basically you'll have two types of missions:
You'll have ones that you can only do solo (where you get to make decisions)
And ones where you can do solo or in a group (where you don't get to make decisions).
The decisions you make on your solo missions affects what missions you get that you don't get to make decisions, leading to overall a much more engaging experience because what you decide to do matters, and how you choose to complete those missions matters.
Not only that, you throw on alot of replay value. People can go through the game multiple times to get all the different missions and each time tell a different story, and change the story of your character entirely.
Of course, you would really have to keep the rewards the same across the board or at least similar, or otherwise people will just go the route for the best. People should be influenced by the experience, not just the rewards.
The problem I see with this is looking at it in the reverse light: If the rewards are different at all, or if the mission is repeatable, people will see this as just a mission you can only complete half of at any given time, not a cool decision making point. I know I would feel obligated to go through the same mission for every possible ending, and I wouldn't see it as a rewarding choice, but just the game forcing me to do two near identical missions for no good reason when i could have spent that time doing two seperate missions. Just a thought, otherwise good premise.