A 20th level Wolverine and a 20th level Thor would be equal.
A more powerful superhero is created in one of several ways (depending on your choice, and which methods you like to use). I'll use Superman and Spiderman as example:
1) Higher level. That's the simple, D&D style method. Superman is 50th level, Spiderman is 15th level (those were numbers pulled out of the air at rnadom, btw, and are not meant to be accurate representaions of those two characters).
2) More powerful templates. Superman has a Kryptonian template, which is ECL +45 or so, Spiderman has the Arachnid Warrior template. You build templates to whatever point cost you choose, while remembering the basic exchange rate of 8 HrPs = ECL +1. Round down.
3) Buying with XP. This way, you just have Superman as a 5th level Specialist (journalist) and lots of superpowers. Spiderman might be a Specialist/Fighter/Rogue with fewer superpowers. Again, each is going to have an ECL depending on how may HrPs you've bought with XP.
The important thing to realise is that all comic book superheroes are not made equal, and it would be silly to pretend that they are. Superman is vastly more powerful than Buffy, for example. There is no reason at all to try and make them equal in HrP cost, levels or anything else.
Also remember that the standard D&D 1-20th level progression is not a typical supers archetype. You can do it with these rules (just run the Hero class as another core class), but these rules are designed to let you choose starting power levels far beyond those of your average 1st level character in D&D.
Also remember that, in the case of HrP ECL equivalence or Hero class levels, you may go beyond 20th level. Normal rules apply for regular classes, though (the Hero class, heroic templates or HrPs do not count towards your character level for that single purpose only, although they do for everything else).