I think this is a great idea.
However, I believe that these should definitely take the place of regular powers. That way, the increase customization. More power pools makes my Sonic/Ice Blaster different from other Sonic/Ice blasters. As it is now, I'm forced to take most of the powers in my primary/secondary because there aren't a tremendous amount of outside options.
making these a separate track just makes everyone more powerful, which is not really something the game needs. Besides, if there are only 5 or 6 background sets, and everyone has one, they aren't going to feel very special.
KK