Geez -- after a read of this thread, I'm almost afraid to post.
I've got a JTV 89F. Picked it up in early November. Special ordered, had to wait for it, probably because most of the local GCs don't carry the 89 OR the 89F (this seems to be the red-haired stepchild of the bunch) and likely because the new batch of 89Fs hadn't yet been infused with version 2.0 yet. I got the guitar new in the box (opened it right there at GC) in tune and with a great low-action setup.
I'd originally assumed I'd get the 59 (since I have a lot of LP-style guitars), but it didn't come with a Floyd. I assumed that the 89 was just there for the metal folks, so I'd ignored it. But when the 89F arrived, I realized that it did a LOT of things the 59 didn't. Access to upper frets (and 24 of them), check. Jumbo frets and a 16" radius -- awesome. NON-baseball-bat neck, just slightly wider than normal (by feel, not by measurement), perfect. Five way (like it better than the hashed-up three-way on the 59), slightly hot pickups, satin finished neck, mahogany body, 25.5" scale. All good. And the Graphtech Floyd. On the money. And they flipped the headstock right side up.
The cons? Metal colors -- black and reddish-black ("blood red" -- cheesy). The alternate tunings lost some of the good ones and subbed in extra down-tunings. Ack. The Line 6 assumption is that this guitar is ONLY good for metal. Stupid assumption. All those models of other guitars vs. narrow-minded (I'm sorry -- "focused?") marketing people. Stupid stupid stupid.
Guitar is flawless. No fret issues (usually the first thing I find), no finish issues. no electronic issues. Obviously they're setting me up for the neck to pop off the body on a gig.
Honestly, I've played all of the others (from the time when Rich Renken was showing me the production prototypes of the original JTVs way back when).
But this may be the best of the bunch.