Duration. Making the action more subtle is useless because you can just use it round a corner, and reducing the cooldown time is pointless because overall you don't get to use the perk any extra times per round (assuming you use it straight away whenever it's available).
Say you reduce the cooldown from 60s to 55s, a match lasts 10 minutes, so you've cut 5 seconds off per minute, which only equals 50 seconds, which still means you can only use it 10 times max.
Two points in exposure time is actually a pretty drastic difference. Without it, you're revealed in an obvious white light for an entire second to anyone looking in your general direction. With it, you show a mildly visible white sparkle for about a tenth of a second, which people might not even notice if they weren't looking at your character.
I'd say it's a matter of preference between (a) 2 points in duration or (b) 2 points in exposure time. Putting one point in each is unlikely to make enough of a difference in either direction, and Disguise's cooldown crafting is so tiny there's no point in touching it.
In the modern world, "common sense" is an oxymoron.