The other possibility is that he's the Doctor from before the Doctor's first appearance. It kinda makes sense that having done something even worse than ending the Time War, he'd choose the name The Doctor and be committed to helping people.
Personally I tend to think that he's the regeneration involved in the Time War is a more likely explanation but the other one is possible. I don't believe he's the Valeyard or any future incarnation because Clara never saw the 12th and 13th Doctors. Plus we all know that the show is going to gimmick in extra regenerations if they ever get to the point where they have to kill the 13th doctor
, so she should have seen the 14th+
Yup, it was the one plothole that occured to me, that the Doctor spoke of the timeline containing Doctors who hadn't existed yet, and yet Clara never saw them and the G.I. never, apparently, attacked them and she specifically stated 11 faces.
At least if it is the 'real' 9th, they can use the excuse that because the War is time-locked, all his actions are inaccessible and unchangeable, hence he could not be touched by either the G.I.
or Clara in that particular regeneration.
The real question, to my mind, is will the 50th be the 'Punishment of the Doctor', or the 'Redemption of the Doctor'

Edit: Either way, I think Trenzalore will be totally ret-conned from the series by the end of it, because there are three questions that still sit in my mind at this stage :
1) Who was the 'just some woman' who gave Clara the Tardis number (probably River Song in the future, since allegedly this was the first time they met, though River has lots of practice at pretending this kind of thing)
2) The self-presented one of Rivers' continued existence after Clara had left (another good reason why this
wasn't her last appearance)
3) The question of the TARDIS' destruction a few series ago, which I suspect is linked to an upcoming interaction with the Time War in the 50th Anniversary, since if there's one group of people who could initiate some kind of self-destruct on the TARDIS, it is the Time Lords.
Edit 2: Also, it's never been cleared up exactly what kind of effect re-booting the entire Universe may have had on the Time War, was it protected from something even as extreme as that?