In TNG, they hid that kind of stuff behind that "fusebox" panel in main engineering, or shoved it into the Jeffries tubes. The new movies keep with the "hide it" philosophy on the "user facing" parts of the ship, but not down in engineering. It seems like a reasonable compromise to me.
I like the hybrid mechanical look. Things that you would need quick and easy access to are there out in the open.
After seeing ST'09 my friend commented, "That's the first Enterprise I've seen on screen that I'd believe had a working toilet."