Hello Chris,
I have to tell you that the trottle response on the 2005 F4 1000 is absolutely crazy: you are absolutely correct in what you are saying....and do you know what I have done? I modified the bike by putting racing pipes, ECU, Power Commander, etc. I truly think i messed up a little bit. The bike is even "snapier" than before and I had to re-learn it: My back tire now drifts pretty much on every tight curve and a couple of times it tried to put the bike into the "high side" position; I was lucky! In my opinion the best modification to resolve this is to bring the bike back to "STOCK" and trust me: it still has plenty of power to be unbeateable on teh track (of course you have to know how to pull all the power out of it).
One day I was at a track day in VIR - VA with Glen Goldman (ex AMA pilot - my personal trainer) and he told me to be carefull because with all that power and the trotte response on that bike, the high side is an easy possibility....especially on that track.
I finally don't believe it is a matter of the year model...instead it's a matter of horse power on a 4 online such as the MV engine; lastly, last weekend I met one of the AMA pilots on the F4 1000: Matt Lynn. He also pointed out that the MV is a bike that you must know how to control; it is definetly a step above many other bikes. The japs in general have better cornering but the MV has the HP on its side.