I would argue that Moffat was just expounding, albeit to the extreme, of plenty of stuff we'd seen through RTD's tenure and even before. The Daleks, the Cybermen, and various other races have always known the Doctor from encounter to encounter over the years. With the beginning of the new series though it seemed more and more that despite being the only Time Lord left (or indeed perhaps because of it), everyone knew who he was.
Whether intentional or not, the stories were less about the Doctor wandering into aliens and monsters he'd never seen before, and more about the baggage he'd been accumulating from multiple meetups with the same, more popular ones. Moffat was certainly part of this situation, and he was right to craft a story arc involving the Doctor getting OUT of the trouble he'd been getting into by being too well-known.