Hmm. I think if the sea did return I'd want some perrilous weather conditions from time to time. Seas that are actually turbulent rather than just having 2D wave sprites wandering past every now and then. I also quite like the idea of having HUGE underwater creatures swimming past and maybe attacing from time to time. The idea of seaing giant underwater behemoths cruise past you while you traverse the ocean is a glorious mental image and would make it seem much more alive. As much as I like the sea from WW it wasn't very lively (for good story-based reason mind you) and I'd like the next possible incarnation of it to be a bit more bustling.
The idea of an upgrade system as rock said is also something I think would make a great addition. Things like a stiffer rudder so steering isn't as flimsy, or a sail that catches more wind so you go faster. Whilst pirating the great sea is an attaractive offer I don't think I'd be too keen on piloting my own huge pirate ships. It would make the experience less personal and no doubt constantly getting off and on the ship would get tiresome. I like the "hop-in" approach they took to KotRL. It meant you could make quick pit stops at islands and not have to worry about things like parking.
See, I grappled with the upgrade system for a bit and tried to figure out what would be feasible upgrades for pirating the open seas. Naturally, I created enemies that would overshadow the likes of a small boat, which meant the only direction upgrades could go is up, But I had no intention of making it cumbersome. By that point in the game, you'd have your hookshot and easy access down and up (if it were a big ship) as your crew would just hoist you up, etc.
Your ship upgrades are:
Sailboat (typical WW style, no canons/no claw)
Merchant Ship (faster, small pirate ship, no canons)
Gale Ship (very fast Merchant Ship w/ 3 canons)
Sloop Ship (your typical pirate ship, Merchant Ship speed w/ 10 canons)
Gun Ship (large and slow-starting, but builds Merchant Ship momentum w/ 30 canons)
and
Thunder Gun Ship (the largest and slowest w/ 100 canons)
The beauty is that they aren't all required for in-game completion. You could manage to do with just the Merchant Ship, but the gun ships are exclusively for those who like to acquire all upgrades and/or blow enemies to bits...literally...to bits. Sailboats and Merchant Ships can be manned by yourself (and so, essentially the Gale Ship as well), but for the gun ships you would need to enlist a crew, which is part of the side quest missions to acquire such a behemoth.
Still, I must remind everyone that the open seas are not the main element of the game. Think of sailing as an equivalent of what Epona was in OoT (not that it'd be that restricted).