The biggest reason I grew to love the FJR's wide ratio 5 speed tranny (vis a closer ratio 6 speed) is the way it allows the rider to utilize the engine's torque to control the bike with just one hand. A closer ratio 6 speed has the rider clutching and shifting more in low speed mountainous wanderings. Sometimes in the Sierra passes (Ebbets comes especially to mind), I like to dawdle and sight see at lower speeds, just enjoying the view or even snapping pics left handed. Seems like the greater low end torque of a big three cylinder would be good for that, while still providing the higher speed long distance comfort we've all come to love with FJRs. If it were to reduce weight, too, then I'd see that as a benefit. In contrast, I don't see slightly narrowing the engine as any big deal.
OTOH, I suspect that a lighter version of the FJR (e.g., using a drive shaft on Yamaha's 900cc triple) might be the perfect sport tourer for smaller stature riders and women. So, in a perfect world, I could see two FJRs based on triples - a 1300 and a 900, both shaft driven, sharing luggage, maybe some drive components, and some fairing/lighting pieces, etc. IOW, all new "His and Hers" FJRs. I don't expect that to happen, and as it is, I'm still plenty happy with my Gen.1 FJR as a standard sized male for whom MC ergos seem most often to be designed.