@Baron: The same issue has existed in AQW for classes with haste skills, so that must've been something unfortunately carried over. More of a bug then a balance issue, but it's definitely a bigger priority in HS considering the importance of timing in PvP.
The best you can do is right now is spam the power button... the skill will cast as soon as its original timer runs out, even if its still showing it in cooldown. Not the best solution, but it's a good workaround until this gets fixed.
Anyway, on stuns. I don't think stuns are so much of a problem themselves as are burst damage combos like Super Intellect, Psychosis, Avra Cadavra and Reality Rend when together with a stun. Three seconds isn't that long of a duration when you consider global cooldowns, that's only 2 powers you can cast in that duration, but with combos like above the only thing that keeps you alive is a well placed heal in between powers. Stuns are great if you catch someone below 50% to kill them before they heal, but you definitely shouldn't be able to bring someone from 100% to 0 during the duration of the stun.
I'd Super Intellect is the big culprit here. If any skill could use a nerf, it would be that.