Vanilla fighter and bomber missions in civ are ridicolously simplistic. The entire air combat system is reminiscent of ground combat in Civ 1 in it's complexity. This is Civ 4, it's time to get with the times.
First off the fighters are an entirely passive force. They simply patrol in neat little circles until an enemy carries out a bomb or recon mission. Pathetically simplistic.
With the new air missions available in many mods you can use your fighters to carry out Fighter Engagement missions and actually attack enemy fighters. This adds a much welcomed layer of strategy to air combat. Now you're forced to split your fighters into Fighter squadrons and Interceptor squadrons, which also enhances the use of promotions.
When I go to war I use my Fighter squadrons (with combat strength promotions) to engage enemy aircraft and sweep the skies for my bombers. Then my Interceptor squadrons (yup you guessed it, Interceptor promotions) settle into orbits around my forward positions to retaliate against enemy bombers and fighters carrying out engagement missions of their own. This is much more realistic and a welcomed injection of strategy to air combat. Furthermore, with limited number of air units in cities and carriers, you'll soon find that Forts are suddenly EXTREMELY valuable and worth building, therefore resurrecting one of the most useless tile improvements in the game.
Secondly, Vanilla bombers. While they achieve their objective, they are still also ridiculously over simplified. With the addition of new missions such as Port Airbomb, Bomb Buildings and Bomb Production they also add a new dimension of strategy.
With Port Airbomb the famous AI strategy of hiding ships in cities, striking out and retreating has been nullified. Port Airbomb allows your bombers (and fighters) to damage and possibly sink a ship in port. Much like in real life, a ship while in port is extremely vulnerable to this attack; thus the chance to sink. This new ability has made safe ports a strategic resource in their own right, and added pressing urgency behind defending your ports so your ships can be repaired.
Bomb Buildings allows bombers to attempt and destroy a random city building. This is a tactic reminiscent of World War II and most recently, Operation Iraqi Freedom. Sometimes hitting an enemy where it hurts doesn't neccesarily mean destroying units.
Bomb Production allows bombers to strip away progress made on a city's build queue. Again, a very realistic operation that has great strategic value.
In my opinion air combat is pathetically simplified in Vanilla civ. While I don't want to micromanage a war I would like to have some strategic choices available to me aside from Intercept and Bomb unit/tile. This is Civ 4 already, not Civ 1.