1. Many skins available in the download section, installable with JSGME.
2. There is no 2?
3. Again, check out the download section, plenty of things to choose from.
4. I'm guessing there are water mods available in the downloads section. Also if you use SH3 Commander (highly recommended!) you can adjust the water clarity in that. In-game water colour or visibility has no effect on AI sensors, or yours other than the Mk. 1 Eyeball.
5. Erm, 16km environment, improved water, much more besides. Even the manual weighs in at some 600 A4 pages compared to the stock manuals lame effort (just the way game packagings are going).
I'm sure someone else will be along to add to this.