Monolith, while game mechanics might only care about the final value, your Game Master and your fellow players are probably more interested in the character the number represents. Or so I hope. Someone trying to tell me that it doesn't matter where the numbers come from, so long as their higher, better, more then someone else, is not involved in a role playing game. Just a math problem.
Also, Superman never struck me as very athletic. He doesn't know how, when, or where to position himself. Pretty much brute forces his way through everything. No running, swimming, jumping, or climbing needed when you can fly. Even his fighting style relies far more upon just being stronger, faster, and tougher then his opponent. Presented in terms of game mechanics, lots of Strength-based Damage, lots of Power Lifting, lots of Flight, Immunity, Protection, Senses, and ranks Enhanced Traits to cover other areas. The moment he encounters situations, effects, and people who can bypass those powers, you're left with a fairly ordinary man who's got good intentions and probably hits Power Level 5, maybe less, with his mundane stats.
Heck, he might even have some unique Advantages, allowing him to use his Movement rank in place of Agility for Initiative, Strength-based Damage or Power Lifting in place of actual Strength for the purpose of a Grapple, and others that allow him to substitute powers for natural capabilities.
Also, let's look at that claim of yours about powers easily 'working around' the system. Let's see here, Movement powers. Wall-Crawling. That's easily two to four power points alone. Speed 1, Swimming 1, Leaping 1. That's ten to fourteen ranks of Athletics right there. Of course, if you want to keep up with superhero folks, you're going to need more ranks of movement then that. Ten points for Wall Crawling 2, Safe Fall, Swinging, Sure-Footed. Covering many of the major uses for Athletics and Acrobatics. Another nine to fifteen points for Speed, Swiming, and Leaping at 3 to 5 ranks a piece. And really, you can't cut out Swimming if you have no Athletics, because anything more troublesome then a calm swimming pool will make you roll checks, and failing one of those gets you to start drowning. Of course, with no Athletics or Acrobatics, you're unlikely to keep up with others when trying to catch a villain in a contested roll. There's also no chance you can win a contest of darts, shoot a good round of pool, play a game of baseball, avoid stepping on landmines, or anything else the GM may decides calls for a Athletics or Acrobatics roll.
Like Superman, you'll have lots of brute force, but little in the way of grace or control. And that might well make for an interesting character, but you haven't worked around anything. You mistake the simple one-note but efficient nature of powers and tell yourself how superior they must be to the 'weak' skills, when they can be used for a great deal more then your powers.