It's fine to want to drop the 3.5mm adaptor. It's old and doesn't have the flexibility needed by modern device which are small and durable to the point where the port itself is prohibitive to size, waterproofing etc. The problem is Apple is absolutely going to be self-serving, they don't want a better standard, they want an Apple controlled standard which is what lightning has always been, it offers no tangible benefit over USB but it costs more and is only usable with Apple products.
So the assumption here is they will use that for high-quality audio and integrate the DAC into the headphones which might have benefits to audio quality given the shorter travel distance for the analog signal (and maybe less noise? I'm not an electrical engineer but it seems possible). The problem is you now have headphones tied to a smartphone vendor (and they won't be cheap) which is unbelievably asinine but this is fantastic for Apple to keep you hardware locked in, and to reap those certification fees, no to mention pushing Beats as the early frontrunner.
There is bluetooth but bluetooth serves a different sort of purpose. It's convenient but not high quality and Apple can't change that without further proprietary bullshit (audio over wifi or something). This is also costly to produce since you need both a radio and a battery. So they aren't going to be packing these in, you're going to get lightning earpods.
Of course they aren't going to strand the market that pays for other headphones, 99% of which are 3.5mm but it's almost certainly going to be a costly DAC that plugs into the lightning port. Maybe they'll market it as "high quality" but like a tumor battery pack it's fixing a problem they created and costing consumers more money.
In the end USB audio could solve all of this, or at least getting some alternate vendor consensus but it won't because Apple won't and that's why this is probably bad.