Are we talking about:
- realistic abilities not implemented yet?
- as out there as possible abilities?
- as fun as possible abilities?
If we are talking about the first, there is so much that could still be done. Some of it might have been done by some games, but never became a staple:
- digging in tanks / hull down tanks.
- exotic squad weapons (automatic rifles, rifle grenades)
- weird inventions that did or did not really work (german remote controlled mines (goliath), remote controlled tanks, flying tanks)
- rare special equipment (steel body armour, special ammunition, field modifications, sticky bombs)
- special training (diving/swimming skills, mountaineers, pioneers)
If we talk about out there... well, the sky is the limit.
- having units teleport instead of being damaged when hit by a weapon (being teleported miles away, into attack range of another enemy unit, or miles into the air )
- transforming units into different units (into frogs, anyone?) when hit
- the ability to fuse units into superunits (very mecha-animestyle, but has it been done in a RTS yet?)
- Units that are affected by spontaneious combustion (so many cheesy references to the classical urban legends about the phenomen possible)
- Units that can move at light speed
- Using micro singularities as weapons (Sluuuuurp! LHC at Cern bringing the apocalypse to your doorstep! Made in switzerland! :))
If we talk about fun, well, that depends a lot on the implementation and the rest of the game obviously