I don't think the 64g has issues - it's just more popular than the 128. When I ordered the 64g through Verizon it was showing a later delivery date than the 128. Personally I don't think I need the extra 64g and wasn't willing to pay the $100 premium. I suspect many others felt that same way. So it's in more demand, and the 128g version has a little more availability and hence comes sooner.
My purchase through Verizon was through work, so I had to wait until 9/22 to order (the company needed to 'approve' the devices for work use) - so my ship date isn't until 11/7. Hoping that moves up.
I suspect Apple makes more money selling the phones direct, than through the carrier who I'm sure gets a cut of the price. While I don't like it (since I have to get mine through verizon), you can't really blame them for trying to make more money.
That is their responsibility to their shareholders after all.