Yeah, I definitely caught the similarities. That was a bit grating, but there was enough of a focus shift to make it interesting. Moriarty is a great villain on Sherlock, to be sure, but The Master on Doctor Who had the benefit of bringing in some interesting backstory that had been hanging for a while (about the Time War and such.)
Overall I really liked the whole bit with The Master. Once I realized who that old guy really was I was pretty psyched. I read a lot of fanfiction and had seen the character crossed into other series; once I picked up on the drums I knew who was about to show up. The Toclafane were just stupid, though, and so was the paradox thing.
How familiar are you with Stephen Moffat's work, by the way? He wrote Blink and is big on Sherlock. It's interesting to watch stuff he's touched because the wife absolutely hates what a lazy writer he is. Moffat just re-uses the same crap over and over again. Literally lifts dialogue from his earlier works and just shoves it into newer stuff he does. I know he does a lot of the later writing for Doctor Who and am curious to see how annoying the wife will be in her complaints when I watch it.