Well, the thing to focuse on to make it work would be the setback of choosing another power; the stronger power, the heavier setback.
And of course you wouldnt be forced to use this, plenty of people are perfectly happy with their villain/hero as it is.
The thing is i had an idea for a villain early on in CoX, and i couldnt create him. He would be a fallen angel, his mind, body and powers vile and twisted. He would wield a cursed, magic sword, and he would defile the spirits of the dead, summoning them as zombies and force them to fight for him... and no archetype fit with this. I could go for the Mastermind (which i intended), but then i would be unarmed, and a ranged fighter whos throwing black goo-balls on his targets... I could have gone with the Brute to get the in-your-face with a cool weapon... but with no defiling of the dead
Anyway, I think the setback should be pretty heavy to avoid leading to a potential cookie-cutter build. For me this would be purely to fit with the theme and story of the villain/hero, and to give a boost to the diversity of CoX