The problem with the idea, is that Perks will become a commodity. People will run up perk points to sell or trade them, and yes I mean sell. It is not uncommon in many Mulitple Player Online games such as "evercrack" for players to sell item on ebay and than transfer them in the game. I would hate to see that. People would just make milk runs to run up their perks and sell them.
Now, as for missions, why not make it an option for the person starting the mission to use his perks alone for all the perk planes in the mission?
I am past the 15,000 perk point mark, hardly ever use them as I like to fly the C.205 and the 110. Now if I could set up a 262 mission, and provide an entire squadron of planes, I would get plenty of people to join.