There are a lot of FJR guys here. With the exception of Dirt_Dad, they pretty much are spot on. Dirt_Dad isn't happy unless he's spinning wheels and being a general hooligan in the dirt, which is not a bad thing, but he's so far off base about the FJR it's really sad. Love you DD, but you're off base here.
I rode an '04 for 160k. Off pavement was no problem. I routinely took it up single track, dual track, gravel, dry river bed crossings, minor water crossings, etc. Part of why I moved to the Super Tenere is because of the abuse I was giving the FJR, knocking rocks off the pipes and just taking it places most wouldn't go. I passed many a parked BMW GS with the ride walking up a road I was riding up. I covered thousands of miles of gravel roads w/o issues. I did upgrade the suspension on the FJR at around 40k. It does make a difference in those less than pristine roads, but I strongly disagree with the opinions that the FJR needs smooth roads.
The FJR is better at wind/weather management in my opinion. That doesn't mean the Super Ten sucks. I rode the Super Ten in the IBR back in July and it did fine. The FJR has you more tucked up in terms of riding position, but that doesn't necessarily equate to less comfort. I sometimes miss the power of the FJR. I always miss the smoothness of the inline four motor. The big parallel twin is a box of rocks compared to the FJR's turbine smooth four. And surprisingly, I miss the electric adjustable windscreen too, though not as much at this point, with 70k on the Super Ten. I changed screens on both bikes, but it's all a compromise. I miss the air flow when it's hot with the S10's fixed windscreen. (Yes, there are manually adjustable options like MaddStadd and Touratech/SWMotech)
It comes down to where you want to ride. The Super Tenere gives you the option of departing pavement with a higher comfort level. Most people are reluctant to take a street bike off pavement to any degree. (It really helps when it's got over 100k, you no longer really care if you drop it). Bonus for the Super Tenere is that you can buy skid plates and crash bars for it, unlike most street bikes. Both bikes get about the same mpg. The FJR has a slightly larger tank and range. The Super Ten has a more upright rider position, but that's really just a matter of what bothers you in terms of knees, back ,etc.
I consider the FJR a better touring bike in many ways. But part of that is because I ride longer days than most. 600-1200 mile days. I feel less beat up at the end of a long day on the FJR than on the Super Ten. The FJR is smoother and more comfortable for me to put in long days on. Obviously, if you're not riding longer days, this may not be a factor for you at all. Almost any bike can be comfortable for 300-400 miles in a day and lots of stops. But riding the bike non stop for 8 hours or more, the FJR is less fatiguing.