Because it's not proprietary enough?

Edit: Original response was a little tongue-in-cheek. More seriously though perhaps they will start bundling Bluetooth headphones as standard. A slim phone plus a "bulky" lightning to 3.5mm adapter doesn't sound like something Apple would do.

Because it takes up lots of space inside the phone? In a phone that thin, the space for a jack connector and its supporting circuitry might compete with another 50-100mAh battery capacity. That's a difficult position for something as obscure as the 2.5mm jack.

The article suggests the phone will also be waterproof. It may be that any kind of jack connector would compromise the waterproofing.