possible rewrite

Okay.  Here it goes.  My character is being called a mary sue.  Truth to be told, he is.  But there is a perfectly plausible (in my opinion) explanation for it.  For one: he's from another universe, and another: his race is of my own creation.  Right now I feel kinda run down about it.  I got some excellent advice and things to read to improve and I want to, but I don't want to completely rewrite my story.  It's really really really hard to do it, I've grown attached to my story and I love it to the point where I'll only fix minor things like grammar or conventions and all that technical yaddayadda.  Anyone who's had it happen to them, please please help.