Well, again, I want to be clear: the USB issue is a temporary software bug that Apple is clearly working to resolve. It should not factor into your decision, in my opinion, AT ALL unless it’s a showstopper for you right now and you only care about it in the short term. And it would only be a showstopper if you refuse to purchase the CalDigit dock in the meantime, since that fixes it for Macbook Pros definitively. So anybody who is taking drastic action or worrying because of the USB issue is, to me, barking up a tree that may not be standing for very much longer, if it’s still standing at all after the update that came out today.
As for Firewire, I don’t have TB3 to verify, but some people report issues, others report none at all. I have an FW800 which I’m running via ADAT and SPDIF into my UCX, so it’s retained a huge amount of value to me given that it’s more than doubled my analog port count for effectively free. It also works just fine over TB2->FW using Apple’s firewire adapter, and I use that to reprogram it in the odd situation I want to switch to the front ports or something.
I’ve had a FW converter fail in the past, and cables make a lot of difference - cables are a wear item, especially FW cables, since a part of their spec and tolerance is the spacing, twisting, and other physical cable properties. If you use a cable too much and/or it was marginal to begin with, it can start causing dropout-like problems. So can the adapters which have exhibited the possibility of randomly dying early in their lifetime. So my guess is that those with issues are likely experiencing the marginal aspects of FW in general, especially through these adapters and maybe old cables, and not necessarily any fault of TB3 itself. But again, it’s a guess. TB3 is more or less just encapsulated PCI, just like TB2, so I cannot see any serious compatibility issues arising there for FW.
However, if you’re really concerned, what I’d do is call the local Apple store, express your concern, and ask if you can trot your gear over sometime. They’ll want you to speak with a business rep or a pro audio rep. Decline their attempts to sell you “lessons” or “pro time” or whatever, and just say you want to make sure it’s compatible with the new devices and ask if they’ll loan you, while in-store, a TB3->TB2 adapter so you can plug your TB2->Firewire dongle in. Try it out on a new Mac with Logic Pro (they’ve always got at least one or two powerful new macbooks and iMacs loaded with that in-store) and see if you get any dropouts. Easy way to verify is just to use a premade loop of some kind that comes with Logic. Bring a couple TRS cables and physically loopback your inputs to your outputs. Play the loops on tracks that output to your hardware’s outs, and re-record the loops on the inputs. If the re-recording is glitch-free, then the audio chain will be. From most reports I’ve read, the glitches are both frequent and non-subtle for FW related issues, so that should give you a high degree of confidence right there.