Well, as I pointed out in a comment to someone else's post, Xander was a sort of Marty Stu at the beginning, so it stands to reason he'd be one again.

I found your points very salient.
I also found the cuts and displacements of this issue very confusing. My respect for Joss as a comics writer isn't all that high--I was underwhelmed by his X-Men too, not that I had a lot else to compare it with.