I don't think you should be ashamed using the Woodland Scenics system. It's very effective! It's not like you open the box and out pops a complete layout, either... You still have to exercise some degree of skill and artistry in the execution. So no, no reason to be ashamed.
You're right in that the track plan is a bit wanting; the over-and-under business will, however, give you a nice long run. My recommendation, if you're able, is to use a bit of flextrack and make that yard in the front look a bit less rigid; maybe add a slight curve to the yard tracks or an extra siding that's not quite parallel to the table edge.
Otherwise, you should be able to make a nice little layout. If the sense of shame comes from the idea that it's a layout kit, I think it's misplaced. After all, if you wanted to build your own design for a 3x6, you'd still need roughly the same materials, right? This way you save money as opposed to buying it all seperately.
Good luck, and heal soon!
