I am not a fan of puffy. I too prefer flat for pretty much the same reasons as you do. I like the way it hangs and looks on the bed.
I however do not do much prewashing except for flannel which I have had shrink up to 3" to 4" WOF. I compensate for my choices by using a medium density quilting pattern when I quilt. So far I have been lucky, I guess, as so far I have not had issues with fabric dyes running or uneven shrinking after washing.
What batting do you use? Do you prewash it as well?