If there are 3 layers (with flannel as the middle layer), you still need enough quilting to hold the layers together. My biggest concern would probably be how the 3 layers will shrink, as flannel is notorious for sometimes shrinking a ***lot*** more than other cotton fabrics. If you have preshrunk all of the fabric (and preshrunk the flannel at least twice), then that would not be as much of a concern.
It's true that a lot of quilting with regular (50/3) cotton thread will stiffen up a quilt. However, if you use a much finer cotton thread (such as Aurifil 50wt 2-ply) or a think polyester thread (such as Superior's Bottom Line), even close quilting will not make the quilt stiff.
I like the amount of quilting you have in the photo. If you do the same amount for this quilt and use one of the finer threads I mentioned (or similar), the quilt will still be nice and soft when you are finished.