I've got no problem with people liking the suit the way it is--I'm not sure I want modifications, myself--but all this garbage about modifications "not making sense" is a load of crap. It is so MIND-BENDINGLY EASY to explain suit modifications that it would hardly be necessary to explain on film. I can do it in two lines:
Wayne: "Lucius, I've outlined some modifications I need made to the suit."
Fox: "Okay."
DONE. Hell, there are plenty of ways it could be explained. Other prototypes lying around? Damage to the original, thus necessitating repairs? Hell, Bruce could educate himself and building HIS OWN version of the suit.
As for WHY the suit would be changed, that's easiest of all: improvements. It doesn't matter if they're technical or just stylistic, because Batman needs both. People say style shouldn't matter to Batman, but how can that be true? We're talking about a guy who goes to great lengths to make himself appear as a Bat demon. Appearance is always going to be at least somewhat relevant to Batman, and as such I don't think it's unreasonable to assume he'd take steps to appear more inhuman or organic.