There are some key new features not available that really is quite great.
1. In LDS.ORG 2.0 you are only logged on in ward & stake websites, with 3.0 you can see how you can stay logged in any where on the website
2. In all places so far, except for the stuff under the tools area, you are able to navigate to other places on the website with out having to go back to the homepage
3. The search bar in 3.0, obviously not complete (as the website is not complete as well) has that search recommendation like on Google and other search engines, something very unlike 2.0
4. In some places, before the color change in 3.0, there was a language "thingy", my guess is that the Church is trying to be done with having the need for multiple domain names. (LDS.org, LDS.org.uk, etc.) Right now, this looks like its being fixed or something.
5. I've also noticed with 3.0, instead of the URL being a bunch of random characters, instead, its nice and clean, something memorable.
Although the site is not complete, its look and new functionality continues be improved upon. This is a project that I keep checking back on & will continue to do so.