From what I understand, Medela used to include soft flanges with their Freestyle pump that were made of silicone. They're discontinued now, but you can get them online for around $20.
Some of the reviews I'm reading say that they are better than the hard plastic flanges because with every pump, the silicone squeezes the breast, so it's not stimulating just the nipple like with the hard shells. Have any of you tried them?