What's the difference to the version 1?
The biggest thing is that it is now completely standalone and runs as its own game. It no longer needs Doom 3.
I don't remember anywhere near all the rest of them, but off the top of my head:
-Lots of AI improvements and a lot of new optional behaviors. (some missions may now have AI that re-light light sources, run for help rather than confront you alone, some missions may have semi-random patrol routes, and so on)
-Several new and better looking models and textures.
-More animations.
-Support for larger maps.
-More voice clips.
-Some physics improvements (notably AI can now be knocked out by falling objects).
There's lots of other stuff, but unfortunately I've been playing 1.08 - 2.00 so long that I don't remember exactly what wasn't in 1.00.
If you're looking for something in particular here's links to all the changelogs:
http://wiki.thedarkmod.com/index.php?title=What%27s_new