I have a Joanns and a Hancocks right down the street where I work. I have only been quilting/shopping these for just a few months so I can't really say if prices have gone up.
My Joanns gripes:
They keep moving stuff around. The batiks, muslin, and homespuns have had about 3 different racks since I've started shopping there. They also don't always mark things on-sale. I don't bring my flyer so I don't always know what's on-sale. I had waited to get a certain cut of fabric I wanted with the 40% off. They told me after it was cut that it was already on-sale, 25% off. So I paid more for it than I wanted. There is also another Joanns across town that I go to once in a while. They carry the 'off-brand' sewing machine feet. The one by work, doesn't. They have a Viking dealer and when I asked for a low shank foot for a Brother, she says that they don't carry those to fit a Brother. I would think that each store would have the same. So I have to make a trip to the one on the other side of town. Also, when both Hancocks and Joanns has 50% off notions, Hancock includes the sewing feet and thread, Joanns doesn't.