I like Moffat and Matt Smith's run in Doctor Who. I love Eleven's quirks, and the standalone episodes are made bearable by his personality. I watch the show to be entertained, and by golly I get entertained. Yes, I am one of those people that was amused by Stormageddon, Dark Lord of All.
But here's the thing that I think separates RTD from Moffat. For RTD, a season-long arc means throwing a buzzword in every episode. Then when we get to the finale, everyone goes "Ohhh, that's what Bad Wolf means." Or "Ohhhhh, that's who Mr. Saxon is." Sometimes he throws in something that was set up by a previous episode, like a fob watch. But the thing is, when you get to the finale, you haven't made up crazy theories as to what Mr. Saxon is, or why Bad Wolf shows up all over the place. Yeah, you want to know, but you aren't disappointed by the reveal being simple because you haven't overthought it in your head.
Moffat, on the other hand, when he puts together season-long arcs, he drops hints in every episode. He makes it a mystery, and people start trying to solve it. And people watching the show want to fancy themselves as clever, so they want some complicated solution they came up with to be right, but they also want Moffat's solution to be cleverer than they are because he's writing the show, so they expect the solution to be a "holy shit, how awesome!" moment every time. But because Moffat's made people invest in this mystery and think about it, people start analyzing screen caps to death, talking about Rubik's cubes and him switching jackets etc. etc. Moffat's presentation leads to people overthinking, so when the solution is simple people are disappointed.
EDIT: Oh, and another thing. Because of Moffat's style, everyone expects answers every episode. Moffat's gotten himself into a Lost debacle, where he's put so many questions/mysteries out there, any time an episode airs and every question the show posits wasn't answered, everyone complained about it. Moffat's clearly got a long-term plan going here for the Eleventh Doctor. Personally, I'm waiting for the Eleventh Doctor to be gone before I start nitpicking what Moffat has and hasn't answered.