I thought of another possibility that might be a little more feasible.
Give Special IOs, Set Bonuses, and maybe even Incarnate Powers each a score, invisible to players, that stacks.
Then have mission difficulty (probably via mob Damage, HP, and Accuracy, but not ToHit) scale with that score.
This way the game stays as it is for people with SO builds but gets harder for everyone else, and scales with their actual Builds.
You could even make having your missions react to this score an optional setting.