"In other parts of the universe, words are science"
"I GAZE UPON THIS BAG OF BONES AND I NAME THEE MARTHA JONES"
"The naming only works once!"
All subjective of course - for me it was an abstract, intangible mess that I couldn't get to grips with. The constant gay allusions with Shakespeare were so trite as well (who was terribly cast).
I agree that the Martha/naming scene was a bit silly, but it is worth noting that entire scene - the Rose reference as well - was written by RTD in 25 minutes because there was meant to be an actual physical fight between Lillith and the Doctor, with her running off at the end to the Globe -- and then during rehearsal on set the woman set to do her sword fighting put her sword into the eye of the guy set to do the Doctor's. The entire scene was cancelled, and they only had that location for one night, so that scene was literally cobbled together in less than half an hour and emailed over, read and learned off tablets and laptops.
I do like the Shakespeare Code, though. The rules for the magic are silly in places, but, er, this is Doctor Who... the rules are pretty much always that way.
I think the main problem with the flesh episodes is that the solely existed to justify and explain the Amy not being there thing. The end result is an episode that isn't rich or interesting enough to support a two-parter but has its content stretched out paper-thin because extra time was needed for the conclusion and such. If you think about the actual structure of that story, for instance, the second Doctor is actually pretty redundant and useless on a story level - there's no need for two of them for the story to progress or conclude, but he provides something fun for Smith to do and provides an interesting plot thread for the second episode.
Funnily enough, I think Lazarus suffered from the same problem, except in a one-parter - because it existed to hint at the Master (with Lazarus' company logo being deliberately similar to Gallifreyan, even though they cut a line where the Doctor comments on it) and justify his ageing technology later on. That's a weird episode as it's actually really over in half an hour - when they blast Lazarus with the machine and Mark Gatiss is there, dead, carted away in the ambulance. The episode could have ended there, but then it sort of pulls the rug out from under you with him coming back to life, escaping and going to the church. That second ending isn't as effective as the first.
For me personally, I think 'Moffat's Who' is far more consistently GOOD than RTD's, absolutely. RTD had higher highs and perilously lower lows, though. I feel like that's reflected in the public as well, really. I feel like that's reflected in the Who-viewing habits of my friends and others around me, too. Moffat has the new popularity abroad to boost him as well, but I feel like in the UK you can see that; people accepted that there would be some shit episodes in 05-10, but Who also had a dominating grasp of the British mindshare at the time. It was something else. For a good 18 months, Who really was the only non-reality should that could make the front pages with relative ease. When Tennant fucked his back and needed that operation? Bloody hell, it was like it was happening to the PM or Prince Charles. The week after the cliffhanger of The Stolen Earth was honestly the best week of Doctor Who fandom I've ever had, because literally everybody was talking about it, everywhere, even people who didn't watch the show. It was something else. I think sometimes the silliness and reaching for something perhaps not as good as it could be on a story level allowed some other people (my mother, for instance, who stopped watching the show during Series 6 because she felt it was getting too continuity-heavy) through the door.
Moffat is no less successful, and ratings haven't dropped - plus he has the international success! I just think Who now has less of a dominating presence in the British hive-mind than it did... but now Americans actually know what the show is, and not in a 'fun joke' way. So, y'know. Different strokes and all that.