"Mandrakes are creatures of darkness. They begin the game with a pain token."
That'd be a nice start, and would go a long way towards fixing them. As would this:
"One mandrake may be upgraded to:
Nightfiend...............-pts
Kheradruakh............-120 pts"
Kheradruakh loses his ability to just appear anywhere on the board (as it is totally useless) but keeps the Decapitator. Any model he chooses as his preferred enemy grants an additional victory point if he kills them in a challenge. Not that useful, but fluffy.
"Mandrakes have the Daemon special rule."
Because why should we get the penalties of the daemon rule against Grey Knights but none of the advantages?
Failing that, make Kheradruakh essentially the Dark Eldar version of Illic Nightspear - independent character, shrouded, any mandrakes waiting to outflank can deep strike withing 6" without scattering, pain token, daemon. It's actually not beyond the realms of possibility. You'd see people buying the stunning models that are mandrakes with just a little jiggling of the rules.
Hopping from terrain to terrain would be a unique idea too. I'd worry that piggybacking them on a unit would make something that has to survive even more of a fire magnet than it already is, so you end up losing the unit carrying them and having the mandrakes just arrive on a board edge or something. But it's cool from a fluff perspective