The wraith feed on life energy. The Pegasis galaxy only has enough humans to support them for long term. The solution they came up with was for most of the population to go into hibernation while a small group stayed active to prevent the humans from attacking the sleepers. When the population sufficiently recovered, the wraith could glut themselves, breed, and go back to sleep. In the pilot for Atlantis, Shephard killed the keeper which triggered the entire wraith population to wake up prematurely. Because of that, the galaxy doesn't have enough people to support them.