My 69 is tobacco sunburst and I think it looks great, the scratchplate is actually a pale green colour but it goes with the guitar great.

Mine was late 2011 manufacture and I did have a few trem problems, but nothing that can't be easily sorted:

1)     the edges of the pivot points espically on the bass string side had burring (rough edges), and this caused it to consistently go flat after going down, but would reset with a slight pull up - taking the trem block out and filing the the burring down to give a rounded edge sorted that out; plus a bit of lubrication helps too

2)     maximum dive is restricted by the cable tie that holds the peizo signal cable in place - the fix for this goes with 3 below.

3)     the peizo signal cable from trem block into the processor did catch as it went through the body or rubbed against the pcb and I could feel it in the trem arm

2 and 3 together were sorted by re-routing the cable slightly similar to http://line6.com/support/message/323936#323936 but rather than the bastardised cable tie I made one myself using a bit of the strong plastic tape that you often find around (not stuck to) cardboard packaging - cut a small length and drill holes to match the trem retention screw.  The reason why this helps with 2 is because the tie-wrap that originally held the cable has the lock part at the back of the block (see before picture on first post) and that takes 2 to 3 mm off the maximum movement of the block backwards; by removing it the trem will go down to where the bottom E is slack enough to be noticably pulled in by the pickups.

Due to headstock shape you can't get the top strings to go slack (locking nut needed), and then neck angle prevents the "perfect" trem raise (to exact intervals) as the trem plate hits the body too early - this can also be fixed by raising the trem up, but to keep the relatively low action the neck will need a small shim to tilt it back slightly.

Even with all this I am still slightly unhappy with the trem, and that is because it doesn't quite "bounce" right; whether it is due to block weight not being heavy enough, the damping foam in the springs, or the damping effect of the peizo cable I don't know, but if you flick the trem the warble isn't perfect to my taste.

On the plus side it work fine for traditional relatively conservative use and the electronics more than make up for it not being a floyd rose.

The reason I went for the 69 was the trem and that's because some of the modelled guitars just wouldn't be the same if there wasn't a trem available - think of the Gretsch guitars.

Same here.  Every time I fired up the 6120 on my old Variax 500, I kept thinking to myself, "yarrgghh! I need a trem!"

I haven't had a single issue with the trem on my JTV-69, but like others who have responded I don't dive bomb; I tend to just use it for smaller bends and vibrato, a la Jeff Beck.

Get a new neck under warranty, put something under the model knob so it doesn't go down so far.

Sorry to be overly obvious, but did you loosen the hex screw?  I think it takes a 1.5mm wrench.  I forget the exact size, but I know that L6 oddly didn't include one with the guitar.