My theory: John Hurt is the Second Doctor.
Rationale: At the end of "The War Games" the Doctor is sentenced to exile and "a change of appearance". By the time we see Jon Pertwee in "The Spearhead from Space" we ASSUME that this follows immediately and Troughton directly became Pertwee.
I assert that Troughton's "appearance was changed" into John Hurt (i.e. no actual Time Lord regeneration), but by the time we see Pertwee, John Hurt has gone through a regeneration proper.
So yes, "Season 6B" theory, but with a half a twist.