Mine is a 99. Changed the front brake pads last year. A few months later, getting cold toward the end of the year, same thing, the stopping power is smooth, but application is notchy. It squeezes, but moves in increments. When I asked someone mentioned old brake fluid and perhaps a master cylinder rebuild. I was looking forward to that this spring but when I brought her out of hibernation, all was good again. I still plan to flush the brakes.
I just rebuilt the calipers on my 98; I had flushed the fluid last year, but thought I would follow up with rebuild. Good decision. There was a fair amount of greasy residue sitting in the caliper/piston cavity. I went ahead and replaced all the seals and pistons. Remember the clutch has the same situation. Mine was leaking, pulled the alternator to make it easier to get to it, replaced all the seals and piston, there was more gunk build up in there as well. Eventually I will replace the hoses/lines as I get to it.
Somewhere in the shop manual it says to completely replace the brake fluid every 5 years. On my old 1993 gl1500 the brakes locked up one day it turned out that the fluid had particles in in and blocked the return hole which I'm told is very small. But before that it also felt jerkey. I would recommend buying one of those small 1 man brake bleeding bottles and pump new fluid through untill it becomes clear. Then I would also do the back ones just on the account of because. If it saves you a breaddown on some lonely stretch of road then it's worth the time spent doing it.
Thanks for the tips. I actually decided that with that and a couple other oddities I've noticed, I'm going to take it to a local bike mechanic I've used a couple times before on my other rides, and just have him check everything over and go from there. I hate to spend the money but Id rather have him do it and have time to ride.