I don't think you can consider Scarlet Witch or Magik Omega level. Their base powers in a vacuum don't stack up to Omega level. They both are being augmented by outside elements, namely mysticism.
Again look at Dazzler (not overly impressive in 616, but her AoA version was nuts), Polaris, Lila Cheney. Not Omega but all very powerful and fairly plentiful, compared to their male counterparts. I'm noticing a lot more powerful (female) Alpha level mutants, which are supposed to be the apex of mutant evolution. Omega's are supposed to be anomalies that randomly have reached the end of their mutation trees.
To add to my point, some more male Omega's (how they outnumber female, I say 3 to 1.); Proteus, The Living Monolith, Vulcan, Mikhail Rasputin (all villains, thus plot devices, but again, we're making sense of it LOL).