The comment is directed at who we eventually find out is VISION. The exact quote is, "Perhaps... imagine a traumatized teenager, X-factor positive and emerging into a full-blown homo sapiens novus. Trying to communicate what they've experienced, by filtered through the fantasies they've evolved to cope." Sounds like he's just trying to describe a new telepathic mutant with an exceptional skill for broadcast telepathy, which makes the use of novus curious. I could understand him using it to describe Geldoff, or maybe even Peter, but I don't believe he did so.
Maybe it was intended to show a difference in the belief systems of Magneto and Xavier... Magneto referring to mutants as superior, where Xavier refers to them as just a new breed of human... but I believe Xavier is also 'guilty' of using the homo sapiens superior tag, isn't he?