Well said.That's what makes Nolan's Trilogy so brilliant. Batman is only really in The Dark Knight: in Begins he's mostly Bruce Wayne trying to create Batman, In TDK he's full fledged Batman who does what he set out to do, in TDKR Batman is older, beaten, broken and unneeded and not what he once was...actually there is no Batman in The Dark Knight Rises, merely Bruce Wayne in a suit. But since Bruce Wayne and Batman are the same person to say Batman is barely in it, i.e., suited up Batman, doesn't make sense.
I don't see how you can say Batman is your favourite character yet your biggest issue is the character of Gotham city which is about the universe Batman exists in, not that exists because of Batman.
Out of Burton's two Batman films I've always found Batman Returns to be more entertaining in it's over the top silliness.