I thought the civ3 concept of aircraft missions was a bit disappointing when I first played civ3, but I have since grown to like it a lot. It makes sense. You can do some additional things with aircraft, like add move points so they can rebase and perform a mission the same turn (apply to ultramodern planes to simulate quick reaction), and make some move as land units, for recon/ground attack craft.
The one thing I would really like to see is the ability to stack bombers into discrete groups and have them mass bombard; in this way, instead of having to attack 30 times with a stack of thirty bombers, you could have 10 in 3 groups, and only have to order 3 attacks on the three cities you want to bomb.
There are some special aircraft that need modified abilities; for example, attack helicopters - these should move as land units but be very vulnerable to AA defenses and fighters. A recon plane should perhaps see the entire swath of land in a straight line between its base and point of recon. There should be special helicopters based off assault ships to ferry Marines inland. And for early warning/antisub patrols, I can see the need for a plane that moves about like civ2 planes. It should be limited to a few turns of fuel, however, and crash if left out from its base/carrier for too long. I wonder if it will be possible to mod in an AWACS type plane, that can see everything for a dozen tiles around? It would be very useful to have a plane like this with a carrier group.