She is the overcomplicated story-arc for the next year or two that will be resolved with a mess of fanwank and/or dismissed with a TARDIS-load of nonsensical timey-wimey bullshit. I can overlook such things though, because she is goddamn adorable.
I think this is about right. I suspect it's just the year's plot (the only one that spanned more than a year is River and that's because she didn't appear every episode).
I think it shall all be revealed in the specials and probably the last one when they hope to have as many as the doctors back as possible.