If you want to know how much the graphics improved thanks the the SCP and FSU teams take a look here:
http://www.hard-light.net/wiki/index.php/GTF_UlyssesThe top picture is from the original, unmodified FreeSpace 2.
If you scroll down to the bottom you'll see the Ulysses in all it's SCP/FSU glory!
Bumpmapping, translucent cockpits with pilot inside, blinking lights on the wings, enviromental mapping (background mirroring from shiny surfaces), animated textures.... you name it the game got it now.
Not to mention a lot of bugfixes and added features (especially for the mission editor FRED).
The only thing I know of that the game doesn't have (yet) is ships casting shadows and ships mirroring on surfaces along with the background.
And as others mentioned before lots of good mods. Some of my favourits (in no particular order) are Blue Planet, Uncharted Terretory, Derelict, Silent Threat: Reborn and the Terran-Vasudan war demo.
Also there is the FS Port which brings the FreeSpace 1 campaign into FreeSpace 2. You might even want to play that before the actual FS2 campaign (followed by Silent Threat:R) to get the full story in the right order without having to read up on it in the Techroom.
There would also be the Drums of War trilogy and Raiderwars, but those are for The Babylon Project, not FreeSpace 2 SCP.
You might also take a look here
http://www.hard-light.net/wiki/index.php/Sample_Lighting_Settings to get the game to look even better. Just pick the one you like most and then copy/paste the settings in the orange lines into the "Custom flags" line under the "Features" tab in the Launcher.