Personally I never upgrade; preferring to do a fresh install each new release. Gives me a chance to clean up the system and start anew. Ofcourse, if this was anything but a worksation you'd probably desire minimum downtime as possible andthe upgrade methog would be ideal.
In my opinion there's no reason why an upgrade won't work..or else they wouldn't have it as an option on the anaconda menu. Ofcourse there will most likely be a few small annoyances to deal with, since this is such a big change from core 1 to 2 (kernel 2.6).
As you say, since the dust has settled, all problems people have had doing the upgrade option have been resolved by now so make sure to immediately update all packages first and if there;s still any lingering issues, there's a good chance it's been brought up here at FedoraForum or other support resources such as the mailing lists.
In summary: Go the upgrade!