Thing is, there's no guarantee at this point 1) that Doctor Who will even return (although I expect it will, and within a year or two at most), nor 2) that RTD will still be in charge (this, in fact, is rumored to be unlikely). Why go to all that trouble to set up stuff that you're not even going to be the person to resolve it? Is this that thing that TV producers do when they end seasons in cliffhangers, thinking that this will pressure the network to renew, inevitably resulting in never-resolved cliffhangers? Seriously, I HATE that. When has it ever actually worked, anyway?
My main gripe with RTD2 isn't the one I've heard from most other folks. It's more that,when he DOES bring back a big-bad, he changes them so thoroughly that they barely resemble the original. The Rani actually worked out fine (bi-generation nonsense notwithstanding), but neither Sutehk nor Omega meshed particularly well with past portrayals (It wasn't lost on me that they NEVER referred to Omega's anti-matter universe, instead using language of "underverse" throughout. Perhaps this helps them to handwave that, originally, Omega no longer HAD a physical body that could become a corpse, let alone a heavily mutated and enlarged one).