Interesting read Blue Gen2
Ive had my gen 1 for 13 years - i came from sports bikes to the FJR and the things i did not like:
1) the brakes needed too much of a pull on the lever (sintered hh pads sorted that)
2) i needed to use the back brake more (you never really use the bake brake that much on sports bikes)
3) the front end feel was vague (this resulted in me get the forks revalved and resprung + replacing the rear shock and + 15mm on the ride height.
All the above changed the bike and it brakes and turns more like a sports bike than a tourer now and i can really get a move on with it, so much so a scare a few sports bikes in the bends.
I still have a R1 but the FJR is my two up R1 at my and my other halfs age. I always thought that i felt that way about the FJR because i came from a racing background on sports bikes so i never really bitched about it. I went about making the bike mine, but it looks like some other people feel the same way, a small amount of magbe but with the FJR's power it means you can overwhelm the standard brakes and suspension if you wish to. But saying all that i still love my FJR even with its few niggles - the build quality, engineering not to mention the get up and go make it a brilliant bike and a keeper.