I think a big difference (though I'm basing this on what I've heard about the way SM operates as a head writer, not actual citable fact) is that RTD heavily rewrote most of the episodes written by other writers and apparently SM doesn't. He sends them back to the writer with notes, but he does not actually do the rewrites himself.
There were a few writers that RTD was under contract to not rewrite, and SM was one of them and I think that's part of why his episodes in the RTD era, as much as I do actually like them (a lot more than I like what he's been doing since he's been in charge), they always felt kind of off, OOC, or too interested in side-lining the established characters/themes for the new ones that he was introducing. While rewatching GITF a couple weeks ago, the people I was watching with and I realised that you could actually replace Ten, Rose and Mickey with Eleven, Amy and Rory and the story wouldn't have to be changed much at all and in fact might even work better since clearly Moffat has his various hobby-horses and seeing them shoe-horned into the RTD era (which had its own, different, hobby-horses) was always a bit jarring. Now that he's free to ride his hobby-horses full-time, having the new characters be a part of that doesn't seem so weird.
Anyway, all that's to say that yeah, I agree. I don't actually like much what SM has been up to, so I tend to like other people's episodes a bit more than his, but the end result is the same, in that it's not hanging together as a cohesive whole as well as it could be.
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There were a few writers that RTD was under contract to not rewrite, and SM was one of them and I think that's part of why his episodes in the RTD era, as much as I do actually like them (a lot more than I like what he's been doing since he's been in charge), they always felt kind of off, OOC, or too interested in side-lining the established characters/themes for the new ones that he was introducing. While rewatching GITF a couple weeks ago, the people I was watching with and I realised that you could actually replace Ten, Rose and Mickey with Eleven, Amy and Rory and the story wouldn't have to be changed much at all and in fact might even work better since clearly Moffat has his various hobby-horses and seeing them shoe-horned into the RTD era (which had its own, different, hobby-horses) was always a bit jarring. Now that he's free to ride his hobby-horses full-time, having the new characters be a part of that doesn't seem so weird.
Anyway, all that's to say that yeah, I agree. I don't actually like much what SM has been up to, so I tend to like other people's episodes a bit more than his, but the end result is the same, in that it's not hanging together as a cohesive whole as well as it could be.