I think if the replacement of the older tech is a standard, then it's not a big deal. Eg. floppy drive vs USB. USB is a universally accepted standard. Sure, Apple ditched the floppy drive on iMacs (they made it external), expecting people to utilize USB ports, then again PCs also have USB ports.
The lightning connector, however, is Apple's own. And anybody making a headphone with lightning has to license it from Apple. And considering it will be pretty much only on Apple iDevice products, I think I can understand why people feel upset.
As for waterproofing, Sony shows that their engineering team has no problem making a thin waterproof phone with a plain 3.5mm audio jack and microUSB, and no flaps either. If this is the excuse from Apple, then I expect the waterproofing of iPhone 7 to exceed Sony's Xperia Z phones.
I have decided to be on the S cycle from now (starting with 6S). Anytime there's a new design, there seem to be a risk of issues (structural integrity, QC, antenna issues, etc). I mean Ive has made great designs, but he's not perfect.
The only thing that would make me want to upgrade right away from my 6S to 7 is if Apple made the iPhone upgrade program available in my country.