I think the main theory is that the Time Lords somehow took the Timeless child(ren?) and somehow stole from them the ability of regeneration and/or time travel, then covered it up. It's also theorized that these may be humans who escaped from the Cybermen as well, implying that the Time Lords were originally human. Like the Toclafane revelation, it would break the Doctor's hearts perhaps. (Although he did get over that and I guess presumed the Toclafane were only a possible future, but this could be more of a problem). Also would kind of solve the half-human thing, although in an unusual way.
But anyway, just a theory/speculation. I and others could be way off base.
Which would be an interesting twist considering in quite a few stories we've seen time lord technology stolen or copied as well, usually with disastrous results (The War Games,Underworld, Mawdryn Undead, The Two Doctors, The Lazarus Experiment).