Helicopters were terribly underutilised in Civ2. I read somewhere recently (can't remember where. Apolyton, perhaps??), that one modern fully-armed chopper is equal to 10 tanks! With that consideration, perhaps there should be two helicopters in Civ3 - one the Vietnam war type, and the other a modern heavy-firepower chopper.
Choppers should be able to carry one unit (infantry variants only), have heavy attack strength but weak defence, and have ability to target building or some equally valuable special ability. This may create a super-unit, but it's weak defence could balance it effectively.
Actually, i believe that there should be upgrades of every unit, dependent on advances that do not form part of main tech tree, like amphibious warfare in Civ2. That way, players are given real choices in tech advances, as they provide an incentive, balanced by temporary suspension of advancing along the main tech tree. You should be able to send a spaceship to alpha centauri without having any of these superfluous unit upgrades. They would remain an option for those who wish to use military options as an alternative. This would add to the depth of the game, by allowing multiple routes to victory. Furthermore, the benefit of super units would be balanced by their short life as state-of-the-art units i.e. the short-term gain of having a super-unit would be balanced by the relative loss on the overall tech tree. Just consider the compound effect of having researched every upgrade tech in an attempt to dominate the battlefield of the day! Simply by not using sparingly, the effect on your science in comparison to other civs (especially peaceful, science seeking civs) could be catastrophic.
Hey, i think this is the answer to many problems with special units. I may start a special thread for this