The classic definition of a Mary Sue is a guest character who overshadows the main characters, who's alleged to be smarter and more skilled and more charismatic than any of them and wins their undying love, but who isn't actually written in a way that demonstrates any of the merits she's alleged to have. Although the term has been broadened to encompass main characters who are unrealistically perfect or undeservedly adored, especially if they're exercises in authorial insertion or wish fulfillment. Bella in
Twilight is sort of the archetypal example of a "Canon Sue" -- although you can make a solid case for Wesley Crusher as well.
http://tvtropes.org/pmwiki/pmwiki.php/Main/MarySue
That's pretty interesting, but it seems to always deal with the two extremes of fanfic characters and canon characters without mentioning the in-between...licensed tie-in literature, where I (who have never read fanfic) first became acquainted with characters who fit the description of Mary Sue in every way except that the fiction in question isn't fanfic.
In the case of a main character like Skye, if you don't want to call the character a "Mary Sue", then there should be another term for it, because it's definitely a flawed character of a particular type. In this case, I'd say the main difference between a character like Skye and an uber-competent main character like Tony Stark (as brought up by another poster earlier), is that in the latter case, the character is successful, perhaps even beyond the creators' expectations, at being well-liked and entertaining to the general audience.
In the case of a character like Skye, there seems to be a gulf between how much the creators seem to like her and how well-liked she is by the fans. The more they try to hit us over the head with how great this character is supposed to be, the more obnoxious the character becomes. Lana held a similar place on S
mallville, though in her case, she had genuine diehard fans to balance out her detractors...whereas I don't see anyone getting too wildly enthusiastic about Skye around here...the reactions seem to all fall somewhere between "meh" and utter contempt.
Also, the type of character in question tends to be a member of an ensemble series who sucks the air out of the ensemble. In the case of a character like Tony Stark, he's supposed to be
the main character in his stories, so of course he gets all the attention.