That's why it's good to have choices.
I'm blessed with the means to have acquired either (though in truth, I would have waited a bit longer if I wanted a GT for the initial demand to wane). I chose the FJR for many, many reasons but one of the keys was because it suited me better with respect to the ergos. In fact, I was prepared to sacrifice comfort in order to get the benefits from the sport-touring package, be it GT or FJR. Turns out the FJR is the most comfortable bike I've ever owned, LT included.
This knee issue isn't only about angle either. MCN pointed out what I discovered in a short test ride: the knee/tank interface is terrible on the GT as compared to the FJR. It's almost impossible to grip the tank with your knees on the GT where as you feel like a natural extension of the bike on the FJR.
I also live in an area (Dallas/Ft. Worth) that suffers from a lack of even one quality dealer. Many here would dispute that fact but it is my reality. Neither Plano nor Ft. Worth is worth a damn to me with respect to sales or service.
Listen, I get the whole BMW thing. I lived it for a while you know
but I'll go a step further on this point: I'd pick the FJR again even if they cost the same. It's literally that good and the advantages of longer service intervals, cheaper service costs, excellent non-power brakes, and a great dealer network make it all the better.
Reviewer after reviewer are saying the same thing: the functionality of these two bikes is neck and neck in virtually every category. But when you factor in that the FJR is $8K CHEAPER
it really is a no brainer.