I rolled back. Here's what I said in another forum post:
I love my JTV Variax! I installed v 2.0 update on my JTV-59 and I have found the following:
* new Teles sound great, especially like the 2 & 4 versions with humbuckers, which are much better than the useless 2&4 models in 1.9
* Spank models generally thinner sounding and 2&4 not as distinctive as 1.9's 2 & 4
* Semi - much cooler sound. I much prefer the 1.9 version which has a warm an resonant tone
* all 12 string models - a touch better than 1.9
After spending ages adjusting amp settings on my POD HD I concluded that , on balance, I preferred the 1.9 firmware and I reflashed my JTV back to 1.9. It was like coming home! Shame to lose the new Tele, but my guitar sounds louder and better now. Maybe it's because I was used to the 1.9 and the change in 2.0 was too much, but for me the poor quality of the Strat and the Semi were deal breakers for me.
There seems to be a lot of superstitious comments in this forum about firmware updates "not taking", but I find it difficult to believe that a digital device can "partially" take a software update. I believe personal preference is in play here and that some people are finding the 2.0 models too thin.
Luckily it's very simple to rollback!