As to the realism debate, it seems that realism for the realism''s sake isn''t a good idea. However, if making a RTS more realistic makes the gameplay experience better, introducing new strategies, then it is a good idea. Theres room for both stricter, more realistic RTS games and looser, more "arcade" style ones, (even though no one plays RTS games at the arcade). For example, some people like to play more challenging, realistic flight simulators, while others enjoy playing games with tons of enemies which they can shoot down quickly generating lots of explosions. I think that there is plenty of room for both styles.

Regarding the air units, I think the best way is the method used in Empire Earth as someone mentioned. You would have, of course, an airstrip or aircraft carrier where the aircraft would stay. Then, if you wanted to go on a bombing run, then you would select your bomber at the airstrip, then you could issue it commands. Once the bomber has completed your commands, it would fly a large stable holding pattern, awaiting further orders and returning to base when it begins to run low on fuel. Then, once at base, it would take some time before the plane was ready to be launched again as it is refueled, and prepped for its next flight. A cost could be introduced for refueling and reloading missiles to keep planes a unit that would be used like real planes are, for specific targeted missions. However, if you only allowed planes to attack for short times at set intervals, then you could give them a great deal of devastating power without tipping the balance too far in favor of air units.

Probably the biggest problem with any air unit implementation in a RTS game is that of map size. Since one of the major strengths of aircraft is that they can attack in a wide range quickly regardless of terrain. Since most RTS game maps are so small, it is difficult to implement this accurately. On one hand, it would frustrate the player when their planes have short fuel capacities and can only strike for short periods of time. On the other hand, planes usually have short periods of time for attacks since they expend so much fuel flying to the battlefield. Its a difficult balance to achieve.