The end of TNOTD pretty much answered the question. He's not a "forgotten" incarnation as the original speculation went since Smith knows exactly who he is. He wasn't worthy of being called "Doctor" which allows him to be one of his past selves which not dirsupting the numbering. (Matt Smith is the 11th Doctor but the 12th body for this particular Time Lord.)
I just hope the Moffat isn't going to have him be the one who ended the Time War as that would contadict Eccleston's entire arc.
Why does it contradict Eccelston's Arc? McGann's Doctor could've changed into the HurtDoctor, who did terrible things during the Time War, and using the Moment (or whatever his final devastating act was) in the Time War could've resulted in HurtDoctor's "dying" and Regenerating into Eccelston, making him born in the Fire of War (or however it was put).
As far as Eccelston, being so surprised about what he looked like, The Doctor is always messed up and confused during his Regenerations, so after having just killed his entire race, he probably didn't get around to loooking in the mirror right away, and the Eccelston Doctor could've been travelling for a couple hundred years without noticing the time had past, or he may very well have Regenerated a mere hours or days before meeting Rose, we don't have any proof either way, other than surprise of what he now looks like
I'm not convinced he is an incarnation between McGann and Eccelston, but, I don't see how that would contradict Eccelston's Arc?