Mind you in no way is this to be read as wrong or to bash the game, it is merely a suggestion to think on. Friends and I have discussed what would take STO to an even greater level than other MMO's plus help avoid repetition that lets face it most any game can get to, be it online MMO or even a console/pc game.
There is an old MMO called Anarchy Online that some may be familiar with. They had a feature in it that allowed any player to go to a mission vending machine. With that they had options they could design the type/style of mission they wanted to play and it would generate a mission, with a small but cool little storyline to go with it. There was several thousands of missions so the maps and story were never the exact same.
We all love the Episodes in STO, but if the Devs looked into something along the lines like this where you could choose a ground base mission, or a space mission, or heck one that combines them, and be instanced into the mission. I personally like the ground missions since there seems to be much less of them than the space ones.
Just a thought, I realize it may be to big a call, but why not at least put it out there?
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They also have a 'genesis' progame in the works, that does something similar to what you suggested.