Like you have the town-terror thing, the base defence, and the final mission..
Well, why not have more types or even absolutely unique missions?
For example
1) a mission where you have to escort villagers out of a raided town
2) a mission to explore a hidden cave where ancient human-kind recorded contact with aliens, to search for some information that could help you defeat the aliens
3) a cooking competition (a la pizza tycoon) against various alien race commanders
4) a mission to raid a special type of alien base where humans are experimented on to rescue some ULTRA ELITE, HUGE PSY-RATING humans which the aliens have captured for study
5) a mission inside an egyptian pyramid or aztec .. er.. something
6) a mission to machu-pichu
7) STEALTH MISSIONS! To install a computer virus on an alien ship/base computer, UNDETECTED.
8) A mission to wobbly bobbly boop