They're not THAT bad if you give them a bit of TLC once or twice a year. I clean my pistons with brake cleaner and a toothbrush, then put some new red rubber grease on and it keeps it functioning well.
I use Ceramic pads on the rear too, to keep the dust down. When i used to use Organic i did notice a big increase in pad dust which can create a lot of the problems.
As mentioned though, the FZS1000 caliper is meant to be a good upgrade. It will need filing in places to make it fit though, but i don't think it's anything major.
That's if you can find one.