This discussion could go on forever without any progress being made. Every person has their own views on what needs to be done to merge the two games. People are sweating over small stuff. T'Leth or Cydonia? Personally, I absolutely could not care less. I play X-Com for the journey, not the destination. I have no interest in stopping the aliens once and for all. I just enjoy policing the Earth and keeping their activities here in check. What happens when you shoot a UFO down over water? What difference does it make? You're assuming that the more land-based aliens breathe our atmosphere, or that they even breathe at all. I reviewed the UFOpaedia entries on the non-robotic EU aliens, and there's nothing saying conclusively that they do (And even if they did, aren't we changing things simply by merging them?) The Sectoids' nose and mouth is almost vestigial at this point, the floaters' respiratory system has been completely replaced by life-support cybernetics, and none of the Ethereals' organs seem to function at all in the first place. Why are we assuming these creatures can't survive underwater? I mean, for all we know, they breathe water vapor, and can just as easily metabolize it in its liquid form. The Sectoids are even mentioned as having aquatic ancestry, after all.
I'm not trying to start another argument on these things, I'm simply saying they're not relevant steps to make a hybrid, and everyone will have a different take on how they should be implemented anyways. Keep it simple. You want to make a hybrid game? You need to do two things. Just two.
1. Allow for the possibility of underwater bases and missions.
2. Solve the color palette issues.
I know that neither of those problems are any small task, but you accomplish that, and I guarantee you that within a month, you'll have a dozen different versions of a hybrid game, thanks to the modding community. Pick your favorite and call it the "official" one, or just cherry-pick and hybridize them to make your own "best" version.
I won't comment too much on solving point #2 above, since I don't know too much about the innerworkings of XC or OXC, except to say that I won't mind if it involves changing the colors of TFTD. Personally, I've always felt its palette was far too... cartoony, for lack of a better word.
As for the first point, that's relatively easy. Allow for a custom World.DAT to be used, one that allows twice as many textures, with a depth assignment to each of them. Anything that's done over a non-surface depth texture (and doesn't have an altitude assigned to it) is marine-based. Then you simply have to create one (or two) variables for everything to declare if it's normal, marine, or amphibious. That's the time-consuming part, because you have to give that variable to EVERYTHING. Weapons, armor, craft, craft weapons, base facilities, aliens, even soldiers and UFO's (For those who seem to thing there should be a distinction between soldiers and aquanauts, and UFO's and USO's, personally it's all the same to me). Even alien trajectories need to accommodate both depth and altitude, to distinguish between a UFO hovering over the surface of the water or a submarine lurking below it.
You do that, and the community will find its own way to merge things, items, technologies, plot.
Done. And done.