Mutations would be hilarious, but I worry that they have too much potential for someone's scripts to go wrong in a wholly non-deterministic way (e.g. a creep losing all of its MOVE components). How would this affect boosts as well?
I like the idea of adding an effect to structures that were under nukes but not destroyed - to actually give incentive to drop nukes on rooms with e.g. 100M ramparts on the spawns. For example;
SPAWN - spawn time increases by ~2 per body part
RAMPART - decays at 5x speed
TERMINAL - cool-down for transactions increases by 10t
TOWER - Add a 1tick cooldown to firing, or reduce max capacity by 50%, or minimum damage range decreases.
EXTENSION - reduce capacity by 10.
Empty space - Creep TTL decreases at 2/tick instead of 1/tick.
I could see this allowing smaller players (lets be honest, firing a nuke is easier than boosting and automating attack squads) to actually apply some real damage to bigger player's rooms, as well as promoting the idea that a room under attack should become more difficult to defend proportional to the number of attacking rooms (e.g. number of launched nukes).
It also adds some neat counter-play - if nukes get launched at your room, instead of building up ramparts to defend, it adds an incentive to move structures.