There are multiple threads with two player variants, and they are great. The biggest change in Gaia Project regarding less players is smaller map. There is an unofficial way to make the original TM map smaller for two players which in my experience of 20+ two player games works perfectly.
Actually there is a second mechanic in place which ensures that a map can get tighter in 2p even if you are playing on opposite sides of the colour wheel: neutral Gaia planets.
Regarding OP: I have already toyed with this idea and will probably return to this thread since I am currently short on time and can't gather my thoughts properly. Essentially I think the core feel of TM should be left intact (that means no coin increase, neutral/lost terrain or dynamic power tokens should be backported, even though I love those aspects), but the scripted nature of openings should be somewhat revitalized by introducing more variety to the setup. One of the best solutions (among others) might be the fan suggested variable cults, I will see if I can dig up that thread at a later time.