I'm thinking something with the displays on the iPhone 6 Plus. I just hope mine is ok. Perhaps backlight unevenness? Image retention? I'm also worried that the thing will bend in pockets since it's so thin and large. Also, the vibration motor is apparently loud on the Plus model, so people will probably complain a lot about that. I'm a tad worried about that as I almost always have mine set to vibrate. There might be something we don't expect, such as the NFC chip going haywire, but I suppose we won't know that until next month when Apple Pay goes live officially.
What's weird is my coworker was at Panera and they had just finished installing new payment terminals. The thing on it said "Tap here to pay" and the old guy ahead of her in line kept trying to tap his credit card against it without success. My coworker asked what they were for and they said "We just installed them for the new iPhone pay." So places are definitely rolling this stuff out pretty fast.