I had a 2004 FJR for 7 years (110.000km) an now own a S10 since december (5000km). Like some people already said, it are completely different bikes.
There are things the FJR is better at (high speed cruising, torque all over, "lazy shifting",...). 80% of my km are commuting (140km/day).
It's a perfect bike for that. 3'rd, 4th or 5th gear on the freeway, doesn't matter, torque all over.
On normal roads you just put it in 3rd gear and you're set for the 50-90km/h range.
The biggest trip I've done on the FJR is Belgium -> North Cape (8500km in 18 days, doing 300 - 1500km a day). The bike is perfect for that, but with a Corbin seat, Helibars,...
I haven't done any big trips on the S10 yet (got it in december) but I think long trips will be easier on the S10. On the FJR you're still leaning a bit forward (especially without the helibars) so you feel it in your wrists and back after 400+ km (especially the day after). Luggage is also a problem on the FJR. When you see it you think "wow, big sidecases". But you realy can't fit alot in there due to the shape. Another thing the S10 is way better at (duh, it's an allroad) is that you can take any road you like. The FJR just likes clean, shiny asfalt (but once on it it's a wonderful bike).
So which one do I prefer ? You just can't compare the two bikes. I'd advise you to lend the two bikes for 2 weekends and do as much km as possible. Take different kind of roads (freeway, twisties,...)