I've suspected this would be the case for months, and now that I finally have my hands on an iPhone 7 Plus and thereby a headphone adaptor I can make my case:
- Most importantly, the headphone adaptor eliminates cable noise caused by using headphones plugged into an iPhone inside a pair of gym shorts or even some pairs of jeans. I've had experience-breaking issues from pants rubbing against the small part of a 3.5mm jack that's exposed on an iPhone 6/6s and very frequently causing static/noise. Downright irritating, but no longer an issue since the 3.5mm plug is fully encapsuled in the adaptor.
- Better sound quality. The DAC (digital-to-analog converter) in the adaptor is better than it was in past iPhones. ~ 10% better, maybe more, with a nice pair of headphones. Seriously, there are audiophiles on the Head-Fi forums purchasing the adaptor to plug into their older iPhone 5/6's just for the audio improvement.
- The adaptor provides a tighter seal, which makes it more difficult for a cable to be inadvertently unplugged. Almost every time I use wired headphones on the 6s while wearing jeans the plug is pulled out at least once while moving my phone in/out of my pocket.
- Just noticed this one: the aforementioned higher-quality DAC the adaptor allows Apple to use also makes the audio output noticeably louder. With a good set of headphones the adaptor's DAC can reach unbearably loud levels.