I can't think of a single instance where the linked brakes took me by surprise or were even noticed much in anything from trail braking to a panic stop.
It became the cause of an accident for me later on when I grabbed too much rear brake while cornering.
ABS and linked brakes are two separate functions, but in the 2007 FJR, the two were inseparable and not optional. But
personally (and controversially) I don't want either, although I will admit that a rider of average skill in typical conditions will probably not find them an issue, and a less skilled rider may well benefit.
In the case of linked brakes, the case is simple: I have been known to get caught in borderline conditions like freezing rain and all too frequently encounter situations like a downhill grade in loose gravel. I want precise control over which wheel gets how much braking.
The benefit of linked brakes is in an emergency situation, where a less skilled rider might just mash the rear and forget the front as his (or her) right hand clamps down in a death grip by reflex. With linked brakes, that rider gets at least
some front brake action in that moment of crisis.
But I maintain it is better to train the rider to use the front brake in the first place (maximizing braking ability in an emergency), and ride with one or two fingers on the brake lever to reduce reaction time instead of relying on that crutch. My fear is that even an experienced rider could allow skills to degrade as the machine conditions them to rely on the crutch during normal riding.
The case against ABS is slightly more complicated. In an automobile, ABS is not a braking aid, it is a steering aid, preventing the wheels from locking up to facilitate maneuvering. The driver simply mashes the brake pedal and let's the computer worry about feathering the brakes. Studies have shown that while minimum braking distances in poor traction situations increase over locking up the wheels, collisions are less likely due to the ability to steer.
On a motorcycle, ABS is of little value for steering. The benefit is in allowing the rider confidence he (or she) can mash the brakes without losing traction in a straight-line emergency stop.
Studies have shown that most average riders will under-brake in slippery conditions (eg: wet roads) due to the fear of dropping the bike. An inexperienced rider with ABS can often stop in less distance than an experienced rider without ABS because the latter initially under-brakes out of an abundance of caution.
So ABS may be -- or even probably will be -- of benefit in a straight-line emergency stop.
However, unlike cars, motorcycles lean into turns. At that point rotational acceleration is not the only force acting on total traction. The computer has no way of calculating the amount of traction remaining for deceleration after the traction of cornering is subtracted. It is entirely possible to slide out due to loss of overall traction with the wheels still spinning and ABS unactivated.
I believe the above is less likely if the rider is skilled at threshold braking manually rather than accustomed to just mashing the brakes and letting the computer work out the details.
I don't want to put words in garyahouse's mouth, but I have to wonder if the results would have been different if he was not expecting -- in fact, conditioned to expect -- the ABS to handle the details when he had his accident.
But that's just my opinion. As I said, Yamaha has shifted the balance from sport to touring over the years. They were responding to market demand, so my opinion is probably in the minority among FJR riders. I never saw the need for a 6th gear or an electric clutch either.