USB vs. 3.5mm, in theory and on a smaller scale in practice, should be no contest. I'm no audio professor, but I do work with telecommunications every day, and I can say from experience that the longer you can keep a signal digital, the better that signal will stay true to it's original form. Once you convert that file to analog at the iPod to transmit over the 3.5mm, it starts to hit some degredation. I know I can notice a difference in USB vs. 3.5mm, in low vs. high bit rate MP3's, and in MP3's vs. a lossless signal or CD's. If you can't, why on earth would you continue to spend money to make your already dirty source try to sound better? I will continue to use digital, USB in this case. Yeah there's way more that comes into play here, but simply put, USB should always win in a contest vs. 3.5mm, except that 3.5mm you can plug into any device.
I just hope those lightning USB cables come out soon, and that these firmwares on the HU's all work with the new hardware/software.