Special mine warheads can work. They'll work better with the next Gold patch IIRC.
"I'm also planning on including a "small XXXXX" for most special armor types (where applicable; picture a Small Organic armor with 6 or 9 hp that regenerates 3hp per turn; would that be workable for Troop and Fighter units?)."
Won't work. Units don't take partial damage; they're either dead or not. And if they're dead, organic armor isn't going to help
Phoenix-D