This doesn't seem to be working in the arena, while testing with Ashido his health was dropping from the custom genjutsu and his chakra was dropping (though whether from the genjutsu or regeneration, I don't know)
It does appear to work on mobiles, as I've seen several low level ones get stunned from exhaustion during prolonged fights since I started using it.
It also seems that unless you're Sand or have purchased Onibi (and possibly Kushin Katsu) that Genjutsu isn't really worth it. Maybe that's just because of the Genjutsu skills I have attached to my custom (Sabaki Stamina, Chakra and Fuyashi) but the drain on the victim doesn't really seem high enough to offset the cost.
Maybe if when your Genjutsu sets in and the target receives the "X slowly evaporates away and the world begins to look distorted!" message combat was stopped and the Genjutsu wasn't immediately visible (Int vs Int + 1/2 genjutsu level roll to detect?) it would be more worthwhile, because in theory the Genjutsu user could reposition themselves and strike. Though currently they are still required to be in the same room to use their skills so it would mostly just be an annoyance.
[FIXED] Sabaki Stamina
Re: Sabaki Stamina
Tested again with Bikku, he confirms that the stamina draining portion isn't working.