But as Christopher Nolan's Batman trilogy shows, that in no way means you have to throw away quality of storytelling.
I would argue there is none to be found in the Dark Knight trilogy. Films 2 and 3 were so full of holes they make the things Trek fans complain about in XI+ seem like nothing at all.
Are you sure it's not simply the more serious tone of those movies you like, instead of the banter and humour of '09 and ID? Isn't that what we had in Nemesis?