The "best at everything" would preclude just about any character outside of fan fiction, except maybe Dr. Who, and render the term pretty meaningless. The original Mary Sue was a teenage girl who was inserted into Trek and solved everything by being great at teenage girl stuff. This is exactly what Skye has been doing.Except Mary Sues are individuals that can solve any situation because they're the best at everything. .
As I stated, she solves situations that the rest of the team can't by looking things up on her cell phone or her tablet. She broke into the most secure mainframe on the planet with a laptop. This week she was so empathetic she accomplished what a trained social worker would need months to do with therapy. I think she fully qualifies as a Mary Sue, she solves far too much with really too little actual skill and training.
If you really can't agree, at least see that this week she was Deanna Troi, only without ANY training, qualifications, or super-empathic abilities.