Oh man, I missed the discussion! Hold up, I know everything about everything!!! (
for once)
You get 2 more usb 3 ports. And an extra processing chip by Asmedia for them.
You get 2 less usb 2 ports.
You get a
vastly more stable esata experience, the jmicron chips are HORRIBLE. I have mine turned off to strip around 8 seconds off the boot time, ugh.
You lose the firewire port and processing chip (by via).
Caps have been moved all around, especially at the pcie slots, showing that the board tracing has been modified.
The VRM delivery system is indeed different, though I couldn't tell you how. I don't even know which one is better.
And finally, the bios chip is twice as big. It also seems to have two differences in the actual firmware standards.
I have the rev 1 sabertooth 990 FX, and have been plagued by system gremlins from day 1. Bootloaders in the wrong place, booting to one drive would boot to another, you don't even want to hear about my ghost uefi install accident. Memory unstable at 1600 Mhz. Ugh.
Bios updates reset the problems, but didn't fix them.
Also. Beware of the old bioses. There was a microcode bug in the FX series which made them incompatible with a number of games on steam (portal 2 would cause a blue screen) and they had to patch it with the bios. It was a DRM function, amusingly enough.
The last version with the problem was 0705. Don't use it!
Hope this was useful, sorry I didn't see this thread earlier.
EDIT: Here's the gallery shots of both boards, so you can look at the caps yourself. Also, the colors are a
little different.
#1:
http://www.asus.com/Motherboards/SABERTOOTH_990FX/gallery/
#2:
http://www.asus.com/Motherboards/SABERTOOTH_990FX_R20/gallery/