The UFO Design 2, and Design one, are quite original and nice.
Even though an UFO could look in any way, most people associate UFO with flying saucers, so 1st model and design #2 are great.
From what I've seen in the "secure the alien ship" mission, the one with the landed ship, that ship looks much like the spaceshutle and less "alien" to me.
P.S. The "guns" on the UFOs look kind of bulky, in contrast with the smooth and "advanced tech" shapes of the craft. Try hiding the barrels a bit.