Hm, difficult question. Both have their plusses and minuses. Agreed with someone above that this question can't really be answered until we get another two seasons (which we hopefully will). On balance, I'd probably say that they pretty similar. However, looking at individual episodes I think seasons 5 and 6 have the edge right now. The Doctors Wife, God Complex, Closing Time... I just love them all. I can't think of many RTD episodes I'd watch over and over (apart perhaps from Blink, and we all know who wrote that).
I love Amy to death, and she's second only to Donna in my opinion. But Rory is awesome. If anything happens to him I'll be devestated.
That highlights my dilemma. Moffat's individual episodes are some of my favorites but his hand at running the whole show has left me feeling sort of flat.