Y'know, I'll admit that's it's probably because I've been falling asleep to version 1.6 ever since I had the marvelous fortune to e-stumble across it, but... I prefer to 1.6 to most of the changes made. Particularly the whole stretch from 3:00 to about 3:33. After knowing and loving 1.6 for so long, that bit was like finding a raisin in a perfectly good cookie.
Here's the thing, though... and I know I'm being a evil, fickle, bastard jerk-face... but I love the opening to version 2.0. I like the opening to version 1.6 more for this song, but I after having just listened to version 2.0, I find myself wanting to hear the whole closing 'setting sail' tune again... Just not at the beginning. Sorry! I'd offer viable suggestions if I could, but my area of expertise lies in people-noise.
First Edit: Jesus H. tap-dancin' Christ on a pogo-stick! Put them together! Like the first 15 seconds from 1.6, then the 2.0 opening!!
Second Edit: So I kinda mulled it over a bit; I like the second half of the Outset Island theme addition, and I really love the Journey beginning. Maybe work Journey into the end...? Something I forgot to mention earlier as well, I DO love the addition of Zelda's Lullaby to the end, that felt like a completely natural ending to the song. Speaking of the ending, one tiny little thing that's irritated me from the beginning-- the piano chord at the end doesn't resolve. And it's just.... gah. >,<