I have a few for ideas for it too:
Bonuses:
I agree with holyknight, its a good idea that maps are giving some bonuses...
My idea is the following: Each map should have a little story and description, and it should give a bonus... For example: Map Tremor has many crates near the human base... Lets imagine that this Tremor is a storage base of vital military equipment... And there is always a big shipment of weapons and armor... If the humans win in this map, then on the next map, they can buy a random weapon or armor 15% cheaper... If Tremor falls into the hands of the aliens, then on the next map, humans can buy a random weapon 15% more expensive, because they have to bring these supplies to frontline from other bases, located far from the frontlines...
OR
If humans win on ATCS on the next map, each human would spawn with a minimum of 100 cred free to spend... So if a human is killed and has no money he will respawn with 100 but if he has more money than 100 when he respawns then this bonus does not apply...
But if the aliens win, on the later maps each alien would start the game with one evo point... And if an alien player dies he will respawn with minimum 1 evo...
Another example: Winning on Nexus Infusion Plant would make battery packs and/or energy weapons 10% cheaper or it would increase the storage capacity of battery packs with +50%...
When the aliens conquer Nexus, then adv maras, would have better zapping damage, or they could zap more far.