This argument works both ways. It's arguable that USB was an improvement over serial and parallel ports for the way those ports were being used at the time. In essence it was able to combine several ports, ADB, PS2, serial, parallel, and allowed the industry to move forward in a more standardized way that was a little more future proofed. However, you point to the complete lack of products on the market at the time Apple made the decision. And that, if you assume nothing else, really the issue behind the removal of the 3.5mm headphone jack. USB was introduced in 1996, yet when Apple introduced it in 1998, and removed all legacy ports, there was effectively nothing on the market available for it. There was absolutely nothing preventing Apple from including the legacy ports on the iMac as well. But their decision not to is ultimately what drove demand, competition, innovation, and price reductions which caused the proliferation of the USB product markets. I would argue that PC makers giving its customers the ability to add USB to their legacy equipment actually slowed the adoption of USB overall. Until a tipping point was reached, where it was more expensive to buy products to use with legacy ports, there was no incentive to buy anything with a USB port. If not for the Mac forcing its customers to buy USB adapters, and replace legacy equipment with USB products, It might have taken a lot longer to become an industry standard.
And that's really in part what's at stake here. For all practical purposes, despite those who love to claim otherwise, there are few Lightning headphones on the market. And to the extent the average customer knows about them, no real incentive to buy them since they are more expensive and the improvement in quality is likely offset by inconvenience of compatibility -- especially since they are playing the same low-res, low-bitrate compressed sound files. BT doesn't fare much better given the state of current technology, not to mention where it was when a consumer may have last tried it. Ease of use, quality, price -- all factors that can't begin to compete with a $10 pair of earbuds bought at a convenience store for many people. So as long as the average consumer has a choice, most are likely going to opt for the cheapest, highest quality product available to them, despite the advantages of the more expensive product.
There's no doubt that wireless headphones are a better experience, all things being equal. Not having to worry about wires limiting movement or getting caught on things, or plugging and unplugging them a dozen times a day, winding and untangling them for storage and use each time. All these things lead to a lower quality experience. And frankly, I would trade charging my headphones once a day for the multiple times I have to go through the cable management routine. Lightning offers less benefits overall, but definitely it allows for higher quality. But as long as there's a cheaper alternative, and no HQ product to listen to over them, then the obvious benefits they do provide like powered noise cancellation, one cable to charge and distribute audio (rather than a redundant audio jack that only does one thing), are not necessarily enough to motivate customers or developers.
Sometimes choice is a bad thing. And I'd argue it definitely would have been for the advancement of USB, and now wireless audio.
