wasteland defense is built around combat and constructing strongholds where rts is more about building and expanding your own settlements and towns.
wasteland defense works like this.
http://www.youtube.com/watch?v=mVcG8U_6M1U&feature=fvst
rts is pretty much the same, but less restrictive to what you can actually build, rts lets you blueprint just about every item in the game to use as materials.
now, if my prediction comes true then sometime after skyrims launch we are going to have a mod that is identical to this or if not very similar.
so what would you do with a mod like this?
build your civilization around a river? up in the mountains? bolster the defenses of one of the main cities? build your fortress outside a city and storm the gates once a day?