Perks earned/death, Perks/sortie, or perhaps best, Perks/time.
Would give a real reward to flying high-ENY low-performance rides other than the perks, which a lot of people don't care about.
However, the current ENY system would have to be adjusted to make sure the high ENY rides really are the more disadvantageous ones and vis versa, as is currently *not* the case with the ENY system.