Hi Isen. Nice to see you posting in the forums. The crashed UFO models you've provided are much appreciated.
I like your models and I agree the supply ship could look more alien. One thing to keep in mind, though, is that when replacing existing models we must reconstruct the geometry in a map editor in order to provide collision detection. Weapons, soldiers, and whatever can move right through models in the map without this extra work. I'm not opposed to replacing the supply ships, but it means that it may not be implemented very quickly because someone (likely ShipIt, myself and mattn) will need to do the work in every supply ship in every map. I don't want to discourage you, but just let you know up-front before you put a lot of time into it.
On the models, I agree with ShipIt and Anderty. The one next to the fighter looks cooler.