I think there should be three modes for customisation:
FORGE: Map maker similar to Far Cry 2's map editor
ANVIL: Game/Scenario Maker you go onto the map and set triggers (Read triggers below)
SANDBOX: A mode similar to Garry's mod where you can experiment with the physics, spawn bots etc.
This next bit is pretty complicated
TRIGGER SYSTEM: This is something of the Age of mythology map maker, it works like this:
You choose an EFFECT like spawn Warthog
And you use a condition like player distance to point
(Now imagine you can get points on Halo and you want to buy a warthog on a particular scenario you have made) The trigger would be:
EFFECT: Spawn warthog at point
Player 1 points=-100
CONDITION: Player 1 distance to point=0
Player 1 point count=100
Feel free to add to or critisize my ideas.