USB 4.0 is coming and it encapsulates Thunderbolt 3. That should solve your Thunderbolt 3 needs.
Giving up x86-64 compatibility doesn't have any downside for Apple at all. Their developers are already split on ARM and x86 development, so consolidating everything to just ARM makes more sense financially and structurally.
It's only a problem with consumers who depend on x86 legacy software. If you're one of these folks, I think the underlying message is: your days are numbered, and you are currently at the mercy of software developers.
As a developer, I'm watching this very closely to see if Apple will still allow me to develop and distribute open-source software on their platform. If not, I'll take my business over to Microsoft promptly. Of all the bad things they are doing, they are still at least allowing open-source software to run on the platform.
I'm watching it but I don't have near-term concerns. I'm running 2014 and 2015 MacBook Pros and, if they go to ARM only with no x86 support, then I'll just get a MacPro and use that for the next decade. I'd just get used MBPs if I needed a new laptop. I think that Apple will get ARM right in a few years. I actually do expect an x86 solution though. If there isn't a great solution, then some of us could get together and build one.