In rough water, nothing will make a ride better than deadrise or the amount of "v" a hull has. Well....there's some other hull attributes, but deadrise is most important. A true deep V hull will slice through waves and make re-entry softer.
Freeboard - the distance from the boat's waterline and the gunwale (the top edge of the upper hull) - is important from a "security feeling" standpoint. In simple terms, it's the difference between feeling like you're sitting on top of a boat and sitting down inside the boat.
As for engines, I don't think there's really much difference between 2-smoke and 4 stroke motors. Let's face it, folks have been using 2-smoke outboards in saltwater for years. Show me ones that have failed Doo to saltwater corrosion and I'll show you an owner that didn't take care of his boat! Consistent TLC is the key.
Having said that, here's something to consider. If you're going off-shore, a SeaDoo boat that has twin engines has a built-in safety feature. If one of the motors craps out, you have another one to limp home on.
Hope this helps. Ask more questions. I don't have all the answers, but I did stay at a Holiday Inn last night.
Tom
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