One of my issues with the RTD era is that it's very kitsch. Of course, it might suit other people's tastes, but personally, I initially dropped it after 3 episodes. I only started watching again after seeing TW S1 and it was definitely an acquired taste. As far as I'm concerned, Moffat definitely upped the quality level of the show.

My other issue is what RTD ended up doing with TW (I'm not sure you've seen it all, so I'm not developing) and how he insulted the fans who were unhappy about it. That one is unforgivable.