I don't think the full upgrade is worth it. But some things are!
I run the 07/08 spec with 808 shocks (you have to use 808 rear shock shafts in front, and XT8 rear shafts in the rear if you do that) but you can just buy the 09 spec shocks now. THAT is a good upgrade!
I have the front upper camber link mod on mine (hard to explain... basically you use a camber link like the rear on the front. Not hard to do) That helps with steering. The 09 spec has that already. THAT also is a good upgrade, and relatively cheap.
The 09 spec has lightened CVDs and the outdrives are different too. Not needed in my opinion, unless you are trying to be ultra-competitive. I doubt the average driver will notice the difference.
The chassis is longer on the new truck, so the center CVDs are different... and it uses the 808 motor mount instead of the older style one. Those are the parts worth upgrading IMHO.
The shock towers, servo tray, and center diff top plate are carbon fiber on the new truck. I actually personally PREFER aluminum, even with the extra weight. If I bought the new truck I'd put the stuff from my old one on it.