From what you're saying i would suggest your brake caliper pistons need a bit of TLC.
One thing people can forget is to keep the caliper pad pin clean as well, i'd give them a clean with wire wool and a light copper greasing, and make sure they're not grooved or bent at all, so that the pads can move freely.
noggythenog suggested a bulging brake line.
I don't know what lines you have, whether they're standard or braided, but my problem ultimately ended up being a faulty braided line which caused an on/off juddering effect, almost like i was breaking on light cobblestones. I still wouldn't have said it was the lines because they were braided, but you live and learn.
If you have standard lines which were bulging i'd guess your braking would feel soft or weak, and may even pulse, it would feel very wrong anyway so i doubt it's that.
On previous bikes the gold coloured bush has worn on the brake lever which can cause a "crunchie" feeling, maybe worth taking the lever off, clean it up and grease it and see if that feels any better too.