the thread is not the only cause of lint build up when quilting- the fabrics and batting all cause it too...polyester creates less lint than cotton...i've found the batts from the dream company seem to not add lint at all- i don't know how/why that is but their batts are magical-and wonderful to work with.
some fabrics are much more (linty) than other fabrics- flannel will really cause alot of fluff. you will find though that it does not matter what you use- you still need to clean the (fluff) in the bobbin area with EVERY bobbin change. it is a combination of all materials being used.
personally- i pretty much never quilt with cotton thread (on top anyway) sometimes i use it in the bobbin- i am much happier with Aurafil or the pro-quilter poly threads. and love using silk- it's expensive though so reserved for very special projects