Is Neill Gaiman really better know by a mainstream audience than the men behind coupling and Queer as Folk?
Grab someone on the street in Phoenix, Arizona or Kelowna BC and ask them who created Coupling, or who created Queer as Folk and they'll give you blank stares.
Ask them who created Coraline or Stardust and odds are they'd tell you. Certainly within the key North American demographic that DW aims at, folks know Gaiman from Sandman and Death and Mirrormask more than Moffat or Davies (who are known, yes, but primarily for DW - maybe also Jekyll for Moffat).
Or not. I very much doubt that BBC Books could pay Gaiman what he can command for an original novel.
I agree, however there's nothing saying BBC Books is the only game in town. Telos and Big Finish both published Doctor Who books within recent years, alongside BBC, Penguin publishes Sarah Jane novellas. IDW publishes graphic novels with no connection whatsoever to DWM. Who is to say a Gaiman script couldn't be picked up by another company entirely. All they need do is pay the applicable licensing fee to the BBC. And frankly BBC Books would probably cough up the money because a Neil Gaiman Doctor Who novel would probably sell more copies than the entire BBC Books range to date, and probably a good chunk of the Virgin/Target line, too. And that's just from Gaiman's established fanbase who'd otherwise never think of buying a Who novel.
I have to disagree regarding Alan Moore. I think he would be brilliant. Don't apply the "Catherine Tate" test to him - condemning him based upon past work and perceived image. He only bitches because companies like DC screw him over for royalties and movie-makers are unable to accurately transfer his work to the screen. If he wrote something specifically for the show, it'd be a different story altogether. And personally I think Doctor Who needs a dark wizard on the writing staff.
Warren Ellis would also be a good choice. So would Moore's partner on Watchmen, Dave Gibbons, another DW veteran.
And at the risk of getting even more eye-rolling, I also hope that good old Terrance Dicks gets a shot. I'd love to see how he'd handle the new series without some of the same shackles he had back in the day (and his Virgin and BBC Books novels shows he's quite capable of writing something other than a 128-page adaptation of The Space Pirates!).
Alex