Never heard of mutants; im such a Geewunner.
Anyway, ive mentioned these before and I know Mkall has picked up on it, but id like to see an expanded use for Intel, specifically in covert missions to steal technology such as taking back the toaster (MKALL!!!) from the bots.
Specific (and rare) missions where the intel of the combatants is taken in to account, and allow the winning team - if their intel is high enough - to gain/steal/copy something from the opponent.
Naturally, my first thought is to use it to raid altmodes off the enemies, but there is also weapon supply raids and energon stealing missions that can be considered depending on how the warpmap is played out and faction stocks etc.
It would allow for those of us who like to RP their minions and try to keep an altmode for as long as possible to do so, gives for a bit of variety within each factions ranks and also give Int a more direct role in a game where things like computers and inteligence raids make up a large part of the expanded universe.
Id also like to see Skill give us ninja powers.