I'm a commercial guy, not a residential expert.... But even I have to agree with the previous comments. You're seeing the wildly excessive wrinkles and mole runs in the felt telegraph through to the finished product. 20,000 thousand nails isn't going to make a bit of a difference, not sure 200,000 nails would do much here...
You may be in a tough situation, the materials have technically been installed correctly, and the finished product is 100% functional and able to perform its job of keeping water out.... So, you're really going to be fighting an up hil battle with the arguement of ascetics. The long and the short, is that shingles should not have been installed over such an uneven surface.
Do you have any way to prove how long the felt was left exposed or if it was subjected to rain / moisture? That would certainly help in demanding the existing be removed and replaced.
I also agree with the comments on felt today being basically junk, it is. Synthetics are the way to go.