What I would like to see is a partisan/guerilla/insurgent unit that more approximates real world guerilla warfare than what we've seen in civ so far.
It should be invisible like a submarine, have the hidden nationality tag from BtS (like privateers), lots of first strikes, the guerilla and woodsman promotions, a good chance of retreating, the pick the unit you target mechanic from BtS (like elephant ballistas [that is if i correctly understand the way firaxis has implemented that feature]), but have a far lower strength that conventional military units. These units should be cheap to build, and use food in their prodution. In large numbers they should be able to bring down conventional military units, but for the most part they should be a nuisance by pillaging and carrying out hit and run attacks rather than a threat to conventional military forces. Autospawning these units from cities with a high revolution index would be a cool feature as well.
To counter these units there should be some type of special forces/counter insurgency unit that can see invisible ground units, have much more strength than partisans, may or may not be invisible, do not have hidden nationality, can paradrop, have amphibious and commando promotions, also have first strikes and retreat, but are fairly expensive.