Sydney Bristow is a bit of a Mary Sue character, 'though. She's special (in a way that seemed to be dropped as a plotline between two of the seasons), fluent in a gazillion languages, a Krav Maga expert, etc.
Olivia Dunham in Fringe has somewhat similar attributes, somewhat toned down, but only slightly.
Both the original and the new James T Kirk are male versions of Mary Sue, which may be why JJA was drawn to the franchise.
Thankfully, the Mary Sue-ness of these characters doesn't grate too much.