I love Connecting Threads cotton fabric. I haven't worked with their flannel. I would bet that it's better quality than Joann's. When I began quilting again the first thing I made was a flannel quilt for my dd. I made it with Joann's. MISTAKE. It has held up but looks like it has gone through the the past 50 years. I made it 5-6 years ago.
So, I'd go with CT rather than Joann's.