It's the pet hair that prevents me from using more flannel! The pale pets shed on the dark stuff and the dark pets shed on the light stuff and all stuff is covered with hair.
I prefer to piece with a 10 myself but will also use 12s, then when I do my quilting on my domestic I go up to a 14 so I buy the mixed three pack needle sets most times. It might seem counter-intuitive, but you might actually try a larger needle first before going smaller, just something the way flannel works for me some times, depends on the weave and the amount of fuzz but that's been more with making clothing and jammies and not quilts.
If you do have a different lighter weight of thread to try on the top that might make a difference too.