My very own Mary Sue

I mentioned a few weeks ago that I am undertaking pretty large-scale revisions on An Unexpected Kingdom, based in large part on advice from my critique partner, Rena.  (Thank you, Rena!)  The critique point that required the most change was one that, while difficult to hear, confirmed a worry that was lingering at the back of my mind: namely, that Ava (my main character) is a bit of a Mary Sue.  In case it isn't clear- that is a bad thing.  A Mary Sue means slightly different things to different people but the basic definition is a character that is entirely too good (good at everything, liked by everyone, special beyond all measure, etc.).  It is generally acknowledged to be a common flaw with inexperienced writers and is often said to be a representation of the person the writer wishes he or she could be.  So, YIKES!  Now, Ava is not the worst of what a Mary Sue can be.  In fact, I took a test, The Original Fiction Mary-Sue Litmus Test, and only scored a 49 of which the test said: 36-55 points: Mary-Sue. Your character needs some work in order to be believable. But despair not; you should still be able to salvage her with a little effort. Don't give up. 
The thing is, and the reason I have been so resistant to altering Ava, is that she is based on an actual person who truly is that great (beautiful, sweet, incredibly smart, talented at everything she does).  Ava is not my cousin Annie, but that is where the inspiration came from and so it seems strange to now pull back and say, "no one is that wonderful", because occasionally people are; Annie is.  BUT, what Rena made me realize is that I can have Ava a generally wonderful kid (although some slight alterations are necessary), but realistically not everyone will like her- because that is truth.  No one is universally liked.  So: revise, revise, revise.  I am procrastinating like you wouldn't believe.  But I don't want to make rookie mistakes, so revise I must.