My educated guess right now: iPhone6 will have NFC. And it will have a secure element, despite Apple having their own "secure enclave".
I don't think Apple really wanted to use NFC. They could perhaps have built a superior experience with iBeacons alone. The problem for Apple is that NFC capable payment terminals are rolling out on a massive scale worldwide, and I think their market share is too small to push an Apple-proprietary alternative, at least outside the US.
The market in the US is special; NFC payments are hardly a thing here, and even those stores that have NFC-capable terminals like Best Buy still turn off NFC functionality (why is a long story...). But if you go outside the US, it becomes more clear that NFC is a standard that is hard to avoid. Canada, the UK, Poland, Turkey, Australia and Japan are just some examples of countries where contactless payment is big, and growing very fast.
So Apple really had two options:
1) Exclusively push their own proprietary solution based on iBeacons. It would probably be awesome, but the problem is that it would require merchants to buy hardware capable of supporting Apple's proprietary tech. Perhaps Apple could pull that off in the US, but it's hard to see merchants investing in it outside the US where their market share is in the 10-15% range. And let's not forget that merchants deploying new payment hardware is not an easy thing: it requires buying and installing hardware, training employees, maintenance and a lot more. Apple would have to come up with an insane value add to justify it - though I'm sure they're working on it
2) Use NFC technology; perhaps not the user experience they were looking for, but good (and rapidly increasing) world-wide acceptance, and the possibility to complement it with their iBeacon-based solution over time.
My only remaining question is whether they will limit NFC functionality to countries where it's already big, and disable it in countries like the US, so they can push their own solution there instead. It would be a weird move, but somehow also Apple-like
Finally, why does Apple need a secure element when they have a "secure enclave"? Because secure elements can be completely powered by the field that is generated by an NFC reader, even when the battery of your phone is dead. Secure Enclave, being embedded in the power hungry A7/A8 CPU, could never be powered that way. Having a secure element would allow Apple to support transit use cases, where "omg my battery is dead how do I exit the subway after I entered with my phone" is a real thing to worry about
Of course I could be wrong; I think not shipping NFC this year would be a big risk for Apple, but they're known to do such things ;-)