I always thought the 8th Doctor (Paul McGann) fought in the Time War and at the conclusion of the Time War he regenerated into Eccleston’s 9th Doctor. This explains why in ‘Rose’, Eccleston’s 9th Doctor appears to be newly regenerated (the scene where he looks at his face in the mirror and talks about his ears).
However, John Hurt’s costume does make him look like a midway point between Paul McGann (the 8th Doctor) and Christopher Eccleston (the 9th Doctor). Although his coat looks like Eccleston’s, the waistcoat and cravat he has underneath are more like McGann.
And so although I do genuinely think Steven Moffatt could insert a ‘forgotten’ incarnation pretty much anywhere in the Doctor’s timeline, if John Hurt is a missing incarnation I think he fits between McGann and Eccleston.
So, what if the 8th Doctor (McGann) 'died' at some point during the Time War and then regenerated into Hurt’s 9th Doctor who ruthlessly destroyed the Daleks and the Time Lords. But his actions were so dreadful that the Doctor realised he had to extract this ‘incarnation’ from himself. I don’t know how he would do this, but it would mean that Eccleston was either:[LIST=1][*]a completely new, replacement 9th incarnation[*]a ‘rejuvenated’ 9th incarnation, where John Hurt’s Doctor took his age back by a few decades/centuries with Eccleston actually being what Hurt’s Doctor looked like when he was young, free from the guilty memories of what his 'older' self had done.[/LIST]One other issue is about how the ‘John Hurt’ Doctor came into existence in the first place. Yes, it could be a standard regeneration triggered by the heroic sacrifice and ‘death’ of the 8th Doctor. But taking into account how ruthless the Time Lords/Rassilon were during the Time War, who's to say they didn't capture the kindly 8th Doctor (who was refusing to assist them) and force a regeneration onto him (as they did at the conclusion to The War Games). Only this time, rather than let the regeneration follow its natural path they manipulated the process to ensure the Doctor's ruthless streak was exaggerated.
Imagine if your greatest weapon in the Time War was the Doctor but his greatest weaknesses were his ethics and his conscience. You’d want a version of the Doctor fighting the Time War free from all that nonsense. And maybe that’s why the Doctor now rejects the ‘Hurt’ incarnation – because he was not conceived naturally.
I do also wonder if this is something to do with the Time Lords' deal with the Valeyard in Trial of a Timelord, offering him the Doctor's remaining regenerations if he was able to have him convicted and executed. Bit weird, in a way, bearing in mind he would essentially be stealing a half dozen regenerations from his younger self. But maybe Moffatt's going to draw on that somehow - that a future Doctor could effectively 'steal back' regenerations from earlier incarnations.