I just swapped out the left side A-Arms on mine and I noticed an extra cross support in the upper A-Arm. And the shock mount on the lower A-arm has changed. Also the grease nipples.
What Johnboy said, but the biggest change is the spindles. They changed the caster on them. The first ones were way too aggresive for most people. I've changed them out on 2 of my suspensions and now I can actually ride them!