I haven't thrown anything away. I always figure I can cut it up and do some improvisational piecing if I'm really not liking something I've been working on.
For problems with seam allowances that just won't lay flat, I've been known to use heavy starch (stay flow mixed 50/50 with water) and smash them with the iron. If they're still not flat enough for my liking after they're dry, I take the top, flip it over onto a board covered with another cloth to protect the top and use a hammer on the backside to hammer the intersections where the seam is bulky. This is an old tailor's trick for working with bulky fabric like denim, but it works very well with quilt tops made of regular quilting fabric. I do this a lot when I've got a situation where lots of seams come together.
Rob