ok the answer is simple. It is not an answer that people like but the the best way to avoid issues with an upgrade.
Go in and do a factory reset
go back in and do the upgrade
do another factory reset
set your phone back up.
Yes it sucks but the first thing that anyone is going to say to you when you have an issue is to do a reset anyway. You can save yourself a few hours of frustration by spending an hour doing it this way.
I say that JB is not that different but worth it is easy. This upgrade is not as wide sweeping as going from Gingerbread to ICS, but the additions in battery savings and "butter" as well as Google Now and a few other options make it worth moving.
I agree that you should be able to dismiss the update if you want, but that isnt the way it is.