Your analysis of the perk points implies that good pilots earn enough perk points to complete various missions. In fact, there are many good pilots with only a handful of perk points, because not every pilot has the same amount of time available to fly. If you have a lot of time to fly you can earn enough perk points, but if you don't you're at a major disadvantage. Coupling this with the fact that both types of pilots pay the same price to fly, and you have the inevitable argument.
If we have to have perks, and in my opinion it's the worst attribute of this sim, then give each pilot the same set amount of perk points available to use up during his monthly tour. When he uses them up he's done, and no accumulating points from month to month. Then if you're good enough to keep the points all month, you've earned the right to fly those planes. If you use them up quickly, you wait till next month.
Don't fall into the trap of automatically assuming that all pilots who have accumulated a lot of perk points are good pilots. Most of them are pilots with a lot of time to fly.
Ranger Bob