I'm not sure I like the taller, squishy footpeg rubbers. The point, I think, was isolation from engine vibration, but I don't think the FJR really needs that. (If it does, it probably needs a TB sync.) Oh yeah- smoother than my Gen I even after a TB Sync. Anyway, I like firm contact with the bike.
Your thumbs will need to be re-educated, especially your left thumb, which controls turn signals, horn, cruise control on/off and set/- resume/+ and the rocker that controls windshield, heated grips, and info displays based on which option is selected by your left index finger.
The headlight rocker is High/Low/Flash.
The "kill switch" is now Off/Run/START. The D-Mode switch is below that, and hazard flashers below that.
A friend with an Gen II says the seat is the same height as his, but it's taller than my stock Gen I. (About the same as my Gen I is, with a Russel Day Long and a stiffer shock that raised the bike about an inch.)
I think there are actually FIVE trip meters. The extra three are designed to be used to track maintenance intervals- they're labeled OIL, FREE-1 and FREE-2. I thought they would turn an indicator on, but right now they all read the bike's current mileage, so I think they're actually mile counters.
Others have commented that the exhaust is deeper sounding than they expected. I've got StainTunes on my Gen I, so I don't have a solid reference point for "stock"- but it sounds a lot like the StainTunes (which will get moved over if they fit).
Dash illumination can be adjusted, but it doesn't control the non-LCD indicator lights- N, ABS, TCS, CC & Set, Hi-beam- which are too bright at night.