I generally like games where the mechanics are designed toward the flavor or an overall feel.
This is an important note. Mechanics create a tone or feel to the game that is independent of the fluff, and where your run into "crunch" and "fluff" not lining up, it is really "tone" and "fluff" not lining up. it's like trying to run a traditional murder myster in D&D with 9th level PCs -- those characters' abilities (crucnh) don't line up with the way a traditional murder mystery plays out (fluff). This isn't to say you can't do murder mysteries for 9th level D&D characters, just that you have to adjust either the fluff (it is no longer a traditional murder mystery) or the crunch (divinations don't work in the the old mansion) to make it work. And that's okay -- those kinds of challenges, when overcome, make for better gaming in general, IMO.
As it relates to the broader idea: game mechanics should support the intent of the game, either the intent of its designer(s) or the intent of those utilizing it for play. Intent is often expressed through the fluff. If these things don't reconcile and there doesn't seem to be a reasonable fix, chances are you have the wrong combination of crunch and fluff.