The perk system IMHO is far and away better than the alternatives tried by AW (which tried nothing) and WB (which tried a highly-skewed RPS). It ain't perfect, but that's fixable. I would like to see how perks are determined, and their price, modified, and the scope of the whole system expanded.
The purpose of the perk system is IMHO to keep certain planes (that HTC probably shouldn't have put in the game in the first place

) from dominating the arena so much that hardly anything else gets flown. The idea is to preserve game balance and the variety of aircraft match-ups in the arena more than it is to reward those who do well.
The planes to perk, therefore, should be planes that can do everything well in air-to-air combat. Planes that have high speed and good turn performance. These currently get used a lot because of these abilities, upsetting the balance struck by planes more specialized for one or the other. Take these planes out of the picture and the other, more specialized, planes will see greater use.
So, if a stallfighter is as fast or faster than most E-fighters, perk the Hell out of it. If an E-fighter can turn with the best stallfighters over a tactically significant speed range, perk the Hell out of it. If a stallfighter is only a bit faster than most of its ilk but still slower than most E-fighters, perk it a little. Also give little perks to E-fighters that are either overly fast with no other advantages, or are one of the best on average AND have some significant advantage in another area.