I think what they might end up going with is having his human dad be some variety of Pacific Islander, and keep Atlantis more or less where people expect it to be. I think it's a great decision and I fully expect Momoa to knock it out of the park.
Making him Polynesian in the comics kind of falls into the "more trouble than it's worth" category. Like, I'd love it if he had always been Polynesian, or if they changed it up for the New 52, because like OP said it's a great connection. But at this point they'd have to do some convoluted reboot nonsense and frankly it's just not worth the headache.
Other points from this thread:
-Kaldur was great, and I'm pretty sure he'll be back as soon as they introduce and Aqualad in the new 52, though they probably won't call him Aqualad because jesus christ who would consent to be called Aqualad?
-Aquaman is, as has been noted, a baller. Man'll talk to the bit of your brain that used to be a fish and give you a stroke. Don't fuck with Aquaman.
-I liked Magog in Johns' JSA.
-Doomsday was cool for a hot minute and then not. Dude has exactly one use in him per reboot, bringing him back after that is automatically a Bad Idea.
-That said, maybe they could retool him somehow. Shit, Prometheus just got his first ever good appearance, so weirder things can clearly happen.