basically, missions could be:
survive for X minutes
kill X enemies
get from A to B
kill all enemies in the level
build a tower X blocks high
defeat the boss (being a huge zombie, a massive spider and so on)
now, of course, this would mean non randomly generated maps for some. specifically number 3 and 4. but, if you added a creative mode to create your own missions and enemy placement, and seeing how the game has had 13000+ purchases, this could take off very well, with loads of maps being made fairly quickly.
The players will also want some kind of award(useful and/or for show boating) for doing these missions. Also there should be a timer so players are racing against the clock to finish the mission and get the best time possible.
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