When Yamaha designed the Venture Royale (launched in 1983), they were one of the first companies to use linked brakes.
They assumed the market for that 800 lb full dress tourer was going to be middle-income guys who were lured away from cars and might have very little riding experience. To make the transition less painful, they linked the rear brake to the front so those who preferred to use the pedal had some chance of slowing down 1000 lb of bike and rider safely.
There were a number of issues with this approach. The guys who bought the bikes were generally fairly experienced riders. It was not anyone's idea of a "first motorcycle". Those riders hated the linked brakes. The other issue was that even when new those brakes were marginal, and linking them in this way reduced the effective front-braking, at least in the way most riders were used to.
Riders solved the problem by de-linking the brakes. This is not hard to do. A new set of braided hoses, bypass the proportioning valve and take the guts out of the valve on the rear master cylinder. No problem. Later they also learned that the front calipers from a Yamaha R6 or R1 would bolt straight on, and the front m/c bore was fine. Finally, half decent brakes.
ABS complicates the matter as it allows for a smoother and better implementation if the brakes are linked. On top of that, the FJR1300 brakes are pretty awesome anyway. They are, after all, designed to haul the thing down from 150 mph in a reasonable time and distance. When we use them in normal riding they are hardly trying, hence the very rapid stops we can make from modest speeds.
The brakes I have on the Gen 1 are awesome ... If y'all are saying that the later Gens are better, then I can't wait
I guess the only real issue is that with such effective stopping power, getting used to using it effectively takes a little learning, and ABS makes that easier.