With licensince issues aside, I'll try to answer concerns accordingly and clearly.
The engine Im using is fairly well set up as-is, and the only coding (I can find a coder in the engine community) that needs to be done is fine tuning. Making a RPG online is simple. With anything (Even here) making any sort of game is hard. There is a reason why Im not coding. I use a GUI engine
You dont make MMORPGs to attact the older generation, who grew up with the origional X-COM. Its as you say Duke, they liked it as it was.
CS does not constitute a RPG. It falls into the FPS category. The determining factor, I think, is game play and goals. In CS, you run around killing people, sometimes try to blow something up or prevent something from being blown up.
In an RPG, there are things to explore, other things to do, and the story to experience.
Very good questions, Yatta. My first thought, which is as easily done and probably better, was to allow players to choose being alien or human. On each side, they would start as basic troops (Humans: Recruit, Alien: Basic of a few of the species), and as they progress, they choose specialty classes (Humans: Promotion, Alien: DNA engineering)
This game would be very PvP (Player Vs. Player), and so the missions would be, for Aliens, would be mostly group assault missions, assigned by local area leaders (How they acheive that position is up to debate), or defending bases or resecuring downed UFOs (Random event). Humans would mostly be defend population (Much like the game), defend bases, capture downed craft, and assaulting Alien bases.
If there is anything I forgot, sorry. by the end of this post, the box was bugging out, making typing difficult