I play exclusively with Merged Mod which adds the aircraft missions I stated above. The time it takes me vs vanilla civ aircraft management is pretty much exactly the same. If you don't like some of the extra bomber missions such as bomb building and bomb production, that's fine. I can see leaving those 2 out of the game as I hardly use them myself. However there are 2 features that are an absolute must have, Fighter Engagement and Port Airbomb.
Port Airbomb negates the exploit of hiding in cities and striking out when your ships are in range. This exploit makes the Blockade option extremely costly, since you're going to lose ships like crazy and you can't even strike back. Port Airbomb allows you to force your opponents to stop hiding inside cities, or to at least seek safe ports where to do their repairs.
Fighter Engagement allows you to seek out and directly engage enemy fighters and bombers. No more passively idling by and doing circles.
Both of these features represent air power much more accurately in civilization. In Vanilla civ airpower is grossly underrepresented, as is it's importance to modern warfare. You can wage endless wars without a thought to controlling the skies, sure you'll suffer some collateral damage but that's what you got SAMs for. Even without SAMs, while your enemy is building bombers, you're building tanks that can take cities away from the enemy. Not to mention there's a limit to how many air units can be held in a city, while there's no limit to how big a stack of tanks you can attack with.
Airpower in civ may seem fine to you Camikaze, but it's an insult to realism. There is no question that airpower is the least developed aspect of civilization, and that's saying a lot.
You are right in saying that aircraft have had a very short history in the scope of human civilization, however for the short amount of time they have been around, their effect on every facet of humanity has been profound. Most importantly in war. America repeatedly teaches it's foes the lesson of the importance of air supremacy.
America's main battle tank has remain largely unchanged for the past 30 years (minor armor upgrades, new electronic suites), same goes for our light infantry weapons (m-16, m249), and artillery units (howitzer). In that same scope of time though our aerospace capabilities have increased exponentially, and secured american military dominance versus any conventional army in the world (they've also given us an incredible edge in operations against irregular forces such as the current insurrection in iraq).
In modern war control of the air space is priority number 1. If you don't control the skies, you lose. It's as simple as that. This may be hard to envision using civilization as an example, but in the real world aircraft currently dominate warfare. It's no coincidence that the bulk of DARPA's budget is aimed at new aerospace technologies, nor is it a coincidence that US ground forces have remained relatively unchanged in 30 years while our air and space assets have gone through exponential changes.
More than words, here's examples of how air assets have completely changed the course of wars (and history):
Enola Gay nuclear bombing of Japan
Israel's Six-Day War (I dare you to emulate this scenario using Civilization and achieve the real-world result, ever)
Gulf War 1
Gulf War 2
Vietnam's Operation Linebacker and Operation Rolling Thunder (proved so effective that Congress began to fear China or Russia's entry into the war)
WW2 Air Supremacy achieved by allies over the english channel (which made D-Day possible)
WW2 Pacific Theatre
WW2 Battle of Midway
WW2 Attack on Pearl Harbor
As these examples highlight, air assets are THE deciding force in modern war. In 1930 Giulio Douhet, an italian air warfare theorist wrote that future wars would be decided in the sky. His theory has been proven true, so true in fact that the United States has the greatest number of aerospace defense contractors and the largest military research budget dedicated to air and space assets.
While I realize that true realism will never be achieveable in Civilization, and shouldn't be, I just cannot and will not agree with Camikaze that air units are well represented. They are an after-thought in civilization, and an absolute non-requirement to waging modern wars.