I love the puckery look of washing and shrinking a quilt after it has been layered and quilted. That's my preference. There are some fabrics that absolutely must be pre-washed however. For example, Batiks will bleed their dye everywhere the instant I forget and don't pre-wash them.
I believe it's okay to mix pre-washed and not pre-washed fabrics in the same quilt top -- puckers, remember. The one thing to overcome when mixing fabric like that is the texture. Pre-washed fabric and fabric straight off the bolt at the store behave differently. Here's why: textile manufacturers use sizing on the fabric to give it more body.
So, to make pre-washed fabric behave like new from the store fabric, use a spray starch when ironing.