Now, while a fantastic DM can just about rewrite any game, change rules, and make water into wine, I contend that a flawed tool is a flawed tool, regardless of how well a skilled artisan can make do with it.
OTOH, if you're holding a hammer by the metal bit and trying to drive in the nails using the wooden handle, then you're using the hammer wrong.
And if you're trying to use a screwdriver to hammer those nails in, then you're really doing it wrong.
"I don't want characters who can fly."
"What system are using?"
"Mutants & Masterminds."
Well, there's your problem right there. You're going to need to do some house ruling or find a different system. But just because Mutants & Masterminds or high-level D&D include rules for flying doesn't mean that they're "broken" or "bad tools" because you're trying to use them without including flying.
(Tangentially, it really bugs me that Oberoni stuck his name on the Rule 0 Fallacy and somehow gets credit for it. From now on I'd like the fireball spell referred to as Craig's Firebloom. Let's make that happen, people.)