The only problem with sailing was how cumbersome it was to change the wind's direction, but making it very simple wouldn't have been the solution for me, I really can't think of an idea to fix it but it lies in the middle.
Besides that and the lack of some big chunk of land instead of scattered little islands the game was awesome from beginning to end but also had a lot of untapped potential to be discovered, more mini quests (NOT fetchquests) like Majora's Mask would have made the game perfect. I still hate link's model, I don't know why but it didn't fit well in the world, it was.. too simple, the facial expressions were great and the eye thing was a really neat idea but still from a pure aesthetic point it was bland and empty, the contrast with characters like the rito, Valoo, Ganondorf or just about anyone else was huge. Zelda, not Tetra, suffer a similar flaw but to a much lesser degree.