Starting with Peter Davison, the ending credit shifted from “Doctor Who” (as all previous Doctors had been billed) to “The Doctor”, with the explanation that this was the character’s proper name. That continued up through at least McCoy (I don’t remember about McGann), then the show ended. When it returned last year, Eccleston was again credited as “Doctor Who” — sending the fanboys into a tizzy, because that’s not the character’s name! How could Davies be so stupid! (This among so many other things, like the episodes being the wrong length and the TARDIS windows being too wide.)
The answer is that it’s almost certainly the proper billing. From the position of an audience member, it’s more precise; where the “Doctor” billing comes from is the incredible sense of literalism that John Nathan-Turner brought to the show in the early ’80s (about the time the show began to go downhill, I’ll note). The science must be “real” science (or at least more credible-sounding nonsense), since this is a serious show; the sonic screwdriver is an easy out for writers, so now the Doctor must find a unique and realistic way to pick every lock; the Doctor is from outer space, so let’s make the intro a starfield to illustrate that; we’re in the Eighties now, so let’s use neon piping for our logo so we’ll look all up-to-date; the Doctor is mysterious, so let’s throw question marks on all his clothes, to illustrate that…
Thing is, there’s a difference between a character and a role. The person in the role of Doctor Who plays a character named The Doctor. It’s not that different from how you’ll see, say, “Schoolboy #1” listed as a role — even though the boy’s friend clearly referred to him as “Jim”. Point is, he doesn’t play “Jim”, or “Pete”, or “Ichabod”, he plays “Schoolboy #1” — whose name might incidentally happen to be “Jim”, or “Pete”. That’s the role he serves in the production. By the same stretch, the role is most unambiguously “Doctor Who”. That this is not the character’s name is kind of beside the point.
After all this, it’s worth noting that Tennant is being billed as “The Doctor” again. The reasoning here is that Tennant, as a long-time fan of the series, insisted, since he’s the one playing the part, that he be credited by the character name. Or the “correct” name, from his standpoint. I suppose that’s his business.