I would like any underwater zone to happen inside a giant glass dome, that is underwater, but not swimming. Vashj'ir was visually very nice, and unique, and played better than anything else they have done underwater before, but it was still far worse than zones that weren't underwater. I think a big zone that you could see things like whales/sharks/fish swimming above you and around the border to the zone would be pretty sweet, but no swimming.
Something like the Eco-domes in Netherstorm, all with different Flora/Fauna linked together with some tubes like the small underwater section of the Tram. It would be cool to have like a dark, damp, sort of Steampunk underground city beneath everything with a bunch of different trams headed to different parts of the zone with a cool scenic underwater path.