If you look at the answer supplied to this question: How did Magneto get his powers back after M-Day? you see that Magneto's powers were restored through the High Evolutionary's extremely dangerous technological procedure.
This suggests to me two things.
- The X-Gene is still a factor for mutants, even though they can't access their abilities.
- A lot of mutants would probably be wanting to get their abilities back.
While there are some who are probably happy to be "normal", I suspect there is a fairly large population of mutants who would be willing to take the same risks as Magneto to restore their abilities. I would also think that Magneto would be one of the people pushing to restore those powers to the mutant population.
So why aren't more mutants gaining their powers back through this process?