I think Bungie will use steep mountains and deep water to cut off world levels. So, I don't think we'll be able to travel by boat or anything.
Do I see there being water in Destiny? Yes. Water that you can walk through? Yes. Whether that be fountains in the last city, a shallow tide coming along the beaches of <wherever>, water crashing into the rocks of Venus, a creek through the jungles of earth, a stream like what we saw on Powerhouse.
But nothing like swimming in deep water, taking a boat out on the waves.
Perhaps, there will be dungeons that are set up like Rapture. Where it's a underwater civilization, or an aquariem type deal, but nothing where you traverse IN water.
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I see your point, and if the oceans weren't instanced it would either add allot of pointless space, or require decades of programming tho make all that water playable.