This should have been so obvious to me.
The first full-fledged Savage Worlds campaign that my group embarked on was a Necessary Evil campaign. I'm actually a huge fan of the Super Powers system, I just don't like it for...superheroes.
While some of the powers have flaws (Decay, as written, is useless in our experience), the overall system just isn't flexible. An OBVIOUS solution was staring me right in the face, though.
The Super Powers Companion offers up Heroic Bennies, which offer benefits not unlike those of the Deadlands Fate Chips, including adding an additional +1d6 to a die roll. I submit an alternate use: Power Stunts.
Your hero can spend a Heroic Bennie to gain the effect of any applicable Modifier for one of his powers, until the beginning of his next turn. The GM has final say over whether or not a Modifier is usable in this manner.
Supers, by their nature, make up crap as they go along...twisting their powers in new and exciting ways. If a PC finds a tactic that they really like? They can pay Power Points to make it a permanent part of their arsenal. Otherwise, they can only bust it out if they have a Heroic Bennie to spare.
Optionally, you can make that a use of any Bennie, not just a Heroic Bennie, if the idea sounds good but limited.
This may have just salvaged "Savage Worlds As A Supers System" for me.