Your idea sounds really interesting, I was thinking myself last night about how to make the game more interesting with more scenarios, and some sort of campaign system.
I think that you are on the right way and I would suggest that after each scenario one heals every surviving character and then you add some special abilities for the dudes. Perhaps something like this:
Level 1: Dodge 1
Level 2: Armour 1
Level 3: Green Dice
Level 4: Red dice
This represents the characters skills improving and their ability to stay alive after each mission. It would also make it more important to keep the team alive and of course would help a lot when the bad guys get tougher.
Are you going to play this like doom with a player playing the bad guys or like the old siege when they "played themselves"?