I'm going with "Both were pretty good," but really it should be more like, "RTD's second season was better at certain things, while Moffat's second season was better at other things." Though I must say that I'm really enjoying the current cast more than the Season 2 cast.
I think the RTD tenure had more episodes that stand out, for better (School Reunion, Girl in the Fireplace) and for worse (Love & Monsters, Fear Her), but Moffatt's has been better in terms of the overall quality and maintaining a solid tone throughout. I vote Moffatt.
Let's do a simple breakdown here... RTD's best School Reunion The Girl in the Fireplace The Impossible Planet/The Satan Pit RTD's worst The Idiot's Lantern Love & Monsters (had a great premise, but went down the shitter halfway through) Fear Her Moffat's best The Doctor's Wife The Girl Who Waited The God Complex Moffat's worst The Curse of the Black Spot Night Terrors Closing Time (I really can't stand Craig) RTD's arc vs. Moffat's arc RTD's arc is pretty tame and subtle especially in comparison to Moffat's (and I can't believe I just said RTD was more subtle than Moffat) but I somewhat enjoyed Moffat's individual entries in his arc than RTD's. Both have a lot of rubbish in them (RTD's space vacuum and WOE IS ROSE!!@!, Moffat's convoluted Silence/Doctor dying/River situation, multiple red herrings), but both also have some good (RTD's Dalek/Cyberman conversation, Moffat's Alex Kingston as River Song). In the end, I think I enjoyed Moffat's arc a bit more because it was more fun (and I don't think it's as complicated as some make it out to be, but it was presented in a bad way). Conclusion I give it to Moffat but only because "The Doctor's Wife," "The Girl Who Waited," and "The God Complex" are so damn awesome (but "School Reunion" and "The Girl in the Fireplace" are pretty awesome, too).
I think I liked Davie's second season better. Season 6 felt somewhat convoluted too me, focusing much to much on the Timey Whimey.
I liked Season Two more than Season Six. Six just had so many episodes I just didn't care about. At least an episode like "Love and Monsters" is still entertaining.
Going with the middle option of "both pretty good" though I do need explain my *actual* opinion... RTD's season 2 and Moffat's season 2 are both about on a par- but the difference is that RTD's season 2 was an improvement on his season 1, cos all of his seasons were better than their predecessors. Moffat's season 2, however, is a step *down* from his excellent season 1...
Moffat, if only cos RTD's second series was probably his worst, especially down to Tennant and Piper's giggling schoolgirl act, not to say it was awful and it does contain one classic (School Renunion) and several good epoisodes (Tooth and Claw, TGITFP, the Impossible Planet 2 parter and the finale is fun) but all things being equal I prefer 11 and co...