If not Borg, there's only one other logical conclusion: Jack is a baby Q.
Basically, Q fucked around with Picard's brain during the events of All Good Things. It was his "gift" to him, because he loved Picard so much and wanted him to eventually join him in the Q Continuum. However, Picard ended up dying from complications instead. Picard passed along his Q juice thing to Jack, who has started manifesting Q powers. Whoever is behind Vadic's faction of Changelings needs Jack's baby god powers to destroy the Federation.
Conjecture in favor:
- Terry Matalas has said that the most popular fan theories are all wrong (which would presumably exclude the Borg).
- It's the most logical/long-running TNG thread to pick up on other than the Borg (who have admittedly been overdone).
- An advanced reviewer has apparently said the end of Season 3 retcons/changes Season 2 considerably, which, if it's not the Borg, means something regarding Q
- John DeLancie said once in an interview that he shot scenes for both Seasons 2 and 3.