While it will be a while before the game can be easily modded, I am designing it with that in mind. Currently all the static value stuff like crafts, weapons, items, aliens, research tree, base layout, etc, are all kept separate from the engine. So the engine treats all that stuff equally. Whether it's a Skyranger or an Avenger it won't care, it'll just look at the values like "soldier capacity" or "acceleration", so you can easily make your own stuff and later it'll all be loaded from XML or something.
I haven't looked at stuff like Lua and external scripting though. I know it's all the rage but I imagine it's a lot more work than it looks, and I'm not sure of the advantage of softcoding everything and turning it into a generic game engine just for moddability's sake.