I know it sounds stupid but... Well, I am used to sounding stupid anyway.
I think of all of the wonderful things Yamaha was able to get right on the FJR. I think of the tremendous amount of engineering it takes to design and build any motorcycle from the ground up. I think about how much thought went into things like the cam profiles, the timing, the throttle body sizing. I think about steering head angle, swingarm length, windshield mechanisms. I think about all of the countless little engineering marvels that make up the cohesive whole that is an FJR.
I'd just bet they had some good reasons for building it with a 5 speed transmission. I'd bet they had ample opportunity to make a change if they found out it did not work they way they wanted it to. I like that 5 speed transmission.