I know how you feel the stock antenna is hideous and I hate the mounting location so a shorty won't work for my personal desires.
GM has a system where the antenna is integrated into the rear windshield similar to the rear window defrosting system. I would love to find an aftermarket version similar to this setup.
I have removed my antenna for now and just have the base attached on the fender. I still pick up the majority of my local radio stations and it's not that big of a deal for me as I don't really listen to the radio that much as it is.
My plan is to find a smaller 6"-8" antenna with a flat mounting surface that I can attach inside the passanger side of the front windshield. This way when I repaint my car I can shave the hole left behind from the base of the factory antenna and give my car the clean exterior look it deserves.