Skulls and Hellions
Sure, some one-off arc that has one of these factions become more powerful. Yet after you finish it, you knock them back down to thier previous, rightful place at the bottom of the food chain.
Well the Skulls never really go away. They're a Nemesis plot.
As for the Hellions, yeah, that'd be cool. The Hellions accidentally summon some big bad that the heroes have to clean up.
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Just go sneak up and beat down one of those little CoT guys take their outfit, and hope no one notice that your eyes are not glowing : P
Actually, a few old ideas I had for improving skulls and hellions included a weird idea for a two sided story arc, one was focused on the Hellions and the other the skulls (duh).
Basically the two bring out the full powers of their respective patrons... And accidentally blow them up.
But the end result is a horrible, mutating disease that slowly and painfully warps the Hellions into crude demons that are growing limbs out of vital organs (or vital organs growing out of limbs), and the Skulls suffered a necrotic disease that slowly turned them into zombies, death knights, and liches.
Both sides gain amazing power, but neither has any control over themselves, nor do their patrons.
They are just blind, suffering, and lashing out, and the disease they wrought is slowly but surely spreading.
Thus, you have a reason why both gangs would go quietly back to the bottom of the food chain, when the alternative is insanity and suffering, getting knocked out and sent to the Zig after a few good runs suddenly seems like a much better choice.
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Azure's idea is more appeasing to me.
The two thug groups have their own magic. They don't need other's magic, they just need to get powerful in their own magic.

sounds good. I've always thought the hellions needed to be more menacing then simple purse-snatching.
I think two group should steal some CoT magic, to become powerful.
Maybe you can fight them again at level 30, or something.
The Hellions can summon the Devil him self, and you need to stop them... or help them as a villian.
Skulls can summon the Grim Reaper, or some deadly dark dude, and you can stop them with heroes or help them with the villians.
What do you think?