Probably one of the easier things to do in order to handle superpowers, especially super strength, is to introduce separate power trees (in the same style as Force powers) which allow the character to deal damage on vehicle or planetary scale if they have super-strength (10x damage), and treat their soak as planetary scale if they have super-endurance (10x soak). You could also build those "power trees" to include upgrades which apply weapon or armor qualities to melee attacks and personal defense.
For super-speed, you could rule that hitting a character with super-speed either increases or upgrades difficulty, or if you're dealing with The Flash or Quicksilver, then hitting them is treated as an Impossible difficulty task (requires a Story Point to even attempt versus a massively-upgraded difficulty, no chance of using more story points to upgrade, though party members could assist). Further powers/talents in that "tree" would allow higher difficulty to hit, more actions per round, and so forth. You might even consider making a speedster's attacks treated as minion groups, in a sense, for how they upgrade and damage against targets (because he's doing so many things "at once", like a minion group would do).
Another option for heroes could be to open up the Adversary talent to them at Tier 3, stackable, and possibly rebranded to "Heroism" or something suitably cool-sounding.
I wouldn't break attribute caps, though, except through Dedication. Especially for super-powers of the same "band", one person having Brawn 3 and the other having Brawn 4 represents not only raw power, but their ability to use it effectively.
I would, though, start PCs with more XP in a superhero campaign. How much, depends on your theme, with 100-125 XP for "gritty" heroes, 150 for city-scale supers, and 200 for planetary supers. Mind, the ACTUAL Superman, Wonder Woman, and Batman, played straight, would start with significantly more XP. Builds based on actual comic book characters should just not care about XP, because they're hard to balance anyway in any serious way.