I was hoping for a dual-butterfly or vacuum piston on the throttle bodies for the FJR since it was a pricey motorcycle -- I guess Yamaha didn't feel it was necessary.
The jump to EFI has made on/off throttle transitions WORSE than a well tuned set of carbs.
In a traditional set of CV carbs, the rider controls the butterfly and engine vacuum controls the carb slide. Because fuel is metered mainly by the slide lifting the needle out of the main jet and the slide is controlled by engine vacuum, there is a smooth transition between on/off throttle. Also, a carb is always dribbling fuel into the engine, helping smoothen the transition.
A single butterfly EFI system is really abrupt. When you twist the throttle, you move the butterfly, immediately and suddenly changing airflow to the engine (there is no vacuum slide to smooth the transition). On top of that, most bikes use a "coasting cut-off" system that completely cuts fuel at zero throttle. So, you get two things when you crack open the throttle from zero. 1) the engine suddenly gets a momentary drop in intake when the butterfly opens and 2) the injectors go from zero fuel to injecting fuel. The engine bogs then gets hit with a lot of fuel. BANG! Super jerky on/off throttle response.
The manufacturers have tried several methods to reduce this problem.
The cheapest way was to use more finely misting injectors. A finer fuel spray allows finer applications of fuel. The problem then ends up being that you can't pump enough fuel at WFO, so they added a second set of injectors. Typically, a lower set for regular riding and a higher mounted upper set for WFO throttle openings. Buell tries to solve this problem by allowing the injectors to stay open at zero throttle like a carb, smoothing the "hit" on open/closed throttle.
This still didn't solve the problem of the butterfly causing the engine to bog when it first opens, so the manufacturers tried to recreate the vacuum slide by either adding another (computer controlled) butterfly or an actual vacuum piston to the throttle bodies in an attempt to maintain consistent airflow.
The latest systems now are throttle by wire, like the R6 of new BMW K bikes. On both, a computer completely controls the single throttle butterfly and opens it to provide fuel.
What makes the throttle on/off transistion even worse is EPA requirements to run the bikes extremely lean.
On the FJR, with its single butterfly, the best we can do is to richen up the leanness which should help a lot. The best would be to get another throttle butterfly in there to help maintain intake velocity and richen the mixture, but that isn't going to happen unless Yamaha does it.
I'm waiting on my FJR, but I doubt it will ever be as smooth as my track bike (ZX-6R with dual butterflies, dual injectors and PCIII which makes the Kawasaki about as smooth as a good set of carbs).