hmmmmm, though this will probably sound redundant to all of you people who have been here for a while and read a lot of the other theories here is my two cents.
First of all, why does everybody imediatly think Vaughn got married, maybe he's just engaged? I realize this really has nothing to do with the two year gap thing but w/e.
Secondly, I forget who but someone said that Irena said that Sloane wasn't the chsen one or whatever, but I remeber it saying that Sloane was a choosen one but Sydney was too.
Third, I believe that Sydney was indeed somewhere for two years and was brainwashed into forgetting what happened in those two years. I don't think Sloane took her because, I don't think he would've kept her alive for two years for whatever evil reason and then let her go, and in Hong Kong of all places, wouldn't he have taken her home? I think Irena is a likely candidate, though for what I have no clue. Also, what if it was Jack? Maybe he wanted to protect her from something that was going on? Though I think Irena is more likely.
Finally, does anybody remeber that episode when someone said that one of the dates on the Rambaldi document was like that night or the next day or something? And I think that i missed the last halg hour of that show, and did anything end up happening? And if it didn't then maybe that 'thing' was Sydney killing Alison/Francie.