It's often overlooked in these discussions, but true: the real heart of a Civ mod isn't the conflict, it's the tech tree. Face it, this game engine is for builders, not for warriors per se. I've begun work on several mods, only to be stymied by the tech tree. There are several ways to approach the problem:
1. You can, as is done in the Jurassic Park Mod and many others, do a token tech tree that is essentially a time-marker. In that case, you have to figure out how many minimum turns each era should have, and make sure that it takes that many turns to research the two or three techs in that era.
2. In a scenario like the one you propose, where there are essentially two disparate cultures in a permanent state of war, and where cooperation and tech-trading are unlikely, you could give each side separate tech trees. Skynet would research techs like bio-robotics, genetics, and facial recognition, while The Rebellion would research things like insurgency tactics, canine detection, and bomb-making. There is a tutorial for making separate tech trees somewhere, I think.
3. The most challenging option is to design a tech tree with trade-able techs that both sides can use, and that moves the story and goals of the game forward. While this takes ALOT more time and thought by the mod-maker, it is ultimately more satisfying for the player, because it gives each side the option to steal techs from the other.
Looking at your avatar, Tommy, reminds me of an idea I had once for an "Escape from LA" mod that would have had a dynamite map and great units, but when I came to the tech tree I literally drew a blank.
I say this not to dissuade you from your idea; to the contrary, I'd like to see it fleshed out a bit: develop a "story line" for your mod, with clear goals for each era. Consider bringing it down to a regional or city-level conflict: there will be more options for the rebellion in limited spaces than in wide-open conflict where air power and big machines have a natural advantage.
