I'd just say it is to seem like something fresh, a new take on an established role and thus using their lesser known (yet still common and recognizable by experts) nicknames rather than their original names, which have been used to great lengths already. Who wants to see yet another Superman or Batman movie nowadays?
Instead Man of Steel or Dark Knight sounds like something different and I think that is quite related to their reboot character, since both movies rather present a completely new take on those stories (Ok, Dark Knight was the sequel to Batman Begins, but so what) rather than continuing the old ones and thus being just another Batman Continues or Superman VI (forgive me for possibly getting those numbers wrong, see what I mean ;)). This is just related to nowadays' popular reboot method of taking a common and established figure and reinventing it (likewise the new Spider-Man is not fourth in line, he's Amazing).
(And it may also be related to the general fact that maybe nowadays filmmakers are more confident of using more metaphorical titles over straight-to-the-point titles than in the past, maybe because we're finally running short of titles? (but this is absolutely unprooved and mere subjective opinion) ;))