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).