Flannels are so hit and miss. I've had it where I used two different colors of the "same" flannel and one pilled and the other didn't. Now I pre-wash my flannel at least twice if not three times...sometimes (not always) I can spot flannel that's going to get weird after a few washings.
So far the only flannel I trust 100% is Connecting Threads. They have really nice thick flannel and so far (knock on wood) I haven't had any pilling from their stuff.
I still love flannel in quilts though and refuse to give it up!