Congrats on the FJR. I think a lot of your initial disappointments were just because you were used to BMW's way of doing things.
It's a great engine on the FJR, now that it's matured a bit.
To me, the bags don't look well-integrated, like they did on the ST1300; that's kind of a shame. But they're not terrible, like the box adv bags.
Does the ES have a "true clutch" like you originally wanted?
It's too late for this now, but did you consider just keeping the BMW and repairing the true mechanical damage and just leaving or touching up the cosmetic damage? It seems not.

The FJR was the best two-up bike (short of a Goldwing) that I've ever ridden. The torque is addictive. Quality was top notch throughout, except that my first gen was kind of hot and buzzy. (all sorted now, as I understand it) I rode it most of the time with just the Givi V46 top box; only took the hard bags for proper touring.