I think what we are talking about is a question of genres. A character like The Ghost is a full-on Superhero in the Superman mold, a comicbook character. But because comicbooks have now annexed film and television the genre has evolved, Superheroes like Wonder Woman, Superman, Captain America, and Stargirl are now closer to fantasy characters thanks to their shift into live-action television and film. And so really are only one step away from Doctor Who as Doctor Who itself is more often than not a fantasy character operating in a fantasy world.
In the original series (1963-89) things were more grounded, the series had internal rules and very defined limits on what genre and content is could and would show. In Doctor Who magic did not exist, Superheroes did not exist, and while from the very start the series played with different story genres and styles (Westerns, Historicals, farce, gritty Quatermass, Satire, Spy thriller, etc.) it did somehow always stay to the same level and honoured its own established rules.
The modern series by Steven moffat's time was much more whimsical, a fairytale world is quite often used to describe the approach Moffatt used for Matt Smith's time on the show, and with the advance in effects and the rise of the Superhero genre to Film and Television it did make a sort of sense for Moffatt to use the new cultural popularity of the Superhero and try to put a Doctor Who spin on it. And as a one-off story, a Christmas special, I felt it worked quite well personally. It surprised me. But as Ancient One outlined down below the Superhero genre just isn't compatible with Doctor Who outside of a throwaway episode like this anymore than Star Trek's universe is... if Star Trek were to do a Superhero episode as with The Ghost, it would, as with Robin Hood and Sherlock Holmes, be entirely within the context of a Holodeck exercise I would say.