If you had to start all over again, which would you use?
I’m just about to complete a major remodel and addition and debating what to add.
I have Lutron for most my switches/dimmers. But thinking of zigbee/thread over z-wave. Also some debate on using matter over WiFi for some devices.
Thoughts?
All of them. 
I don't really see a reason to choose when the hub supports them all.
Lutron is turning me off a bit with how protective they are being with access to what integrations for RA3 would need, including Hubitat (but Caséta Pro, Radio RA2, and similar systems of that generation are safe, as the existing telnet interface is available). And their proprietary Windows-only programming software for the higher-end systems is a bit of a pain, but I suppose not a concern if you go through a dealer instead of trying to DIY it. (Caséta is programmable via the mobile app and bit less clunky, IMHO.)
For Z-Wave, if I had to start new, I'd probably pick all 700- and 800-series devices with LR support if available and avoid 500 and earlier just due to worse battery life and slightly better mesh range you should get even with 700/800 in mesh mode -- but I still have devices of various recent generations (I think all my 300/400 devices are gone, though! and those might make sense if they are repeaters, as their max speed is less).
I don't really see any significant practical differences between Zigbee 3.0 and ZHA 1.2, and I have various devices on both with no problem or difference.
I mostly avoid Thread since it competes with Zigbee and Wi-Fi for 2.4 GHz, and I'm not exactly racing to see how many uses I can find for that frequency in my home, but I have a few just for fun. With Matter over Thread (my only Thread devices), they work fine with Hubitat. In the future, I imagine many manufacturers will make more Matter over Thread devices than Zigbee devices unless they're deeply invested in Zigbee (Philips Hue?), but it will take years to know if Matter will really catch on and with what "physical" layer(s) or Bridges, etc. I don't think Zigbee is going away regardless.
Wi-Fi is my least preferable protocol for this kind of thing, but it depends on the device; there are some where it is really the only option that make sense. For battery devices, it tends to be too power-hungry for practical use (you may notice most/all battery-powered Matter devices are Thread), but for things like a camera or even a weather station with any complexity to the data, there isn't much else. Naturally, I avoid devices with a cloud-only or proprietary API whenever possible in favor of documented, local APIs or Matter over Wi-Fi.
Some people may have a preference for one over the other for whatever reason (e.g., Z-Wave if 2.4 GHz doesn't work well in their environment, but Zigbee and Thread are still supposed to be pretty good at navigating this). But I have all of the above, and I don't see myself moving everything to one any time soon when I have a hub that supports them all -- and I'm not even sure I could if I tried given the varied nature of my devices/
Honestly was just contemplating this- not that I’m starting over again but I did about 2-3 yrs ago w zwave and don’t regret it. I know people will also say that you don’t have to pick a protocol just pick the device that fits the bill but to me it makes sense to have a cohesive environment.
So in short if I were going to do it all over again tomorrow I would go zwave again.
Like @bertabcd1234, I have never stuck to a single standard. I use Lutron, Zigbee and Z-Wave. For Z*, I try to setup my switches so that I will have a good and strong mesh to allow my remaining battery operated sensors to function well.
On a side note, I am really eager for Inovelli to come out with their mmWave switches!!! I plan to remove and replace several sensors with those.
The one issue is building out a mesh for each protocol. I guess I can do both zigbee and zwave but wish it was easier to have the meshes span a larger house.
I have wifi everywhere and will have a separate VLAN for iot items.
I agree about RA2 but I have about 100 caseta switches, picos and motion sensors across two pro hubs. My concern has been fan/light controllers. Otherwise they are rock solid.
I will likely stick with Ring (and zwave) for the alarm, unless there is something better in the next few months.
I’m mostly 800 z-wave with a few 700 items. I’ll have to add outlets/plugs to get the mesh everywhere.
All of them...Lutron for lights, zigbee and z-wave for everything else with a smattering of wifi (as long as it's local)
I would not use zigbee as I find it unreliable (others certainly disagree). I now avoid z-wave for lighting largely because it needs a hub to function, but I do use it for plugs and sensors (Ring repeaters make that possible). I avoid wifi as I don't want to slow down my wifi network. I love Lutron Caseta's reliability but am annoyed at their dimmers, which come on to full brightness and can't be configured to a lower brightness level for the initial "on" setting using the physical switch, beyond a very modest "trim" adjustment. They could easily fix that, but choose not to do so. They also allow only one device to function as a repeater. So close, yet so very far, from being perfect as a lighting system. We just finished a new home less than a year ago and did use Lutron, but it was a "least of evils" choice. I guess I need to learn more about Matter, because there's just no perfect choice amongst the others.
Put me down in the "all of them" group.
When we started (re)building our new house in 2022, I already had one houseful of RadioRA2 and Zigbee, with good experience (including Lutron L2 training) with each, so that's where I started. Upping to RA3 didn't offer us anything new that we actually wanted, and that decision is looking better by the minute, all things considered.
As we built out this house, things changed a bit - no battle plan survives combat, y'know. 
I couldn't get some of the far-flung sensors reliable with Zigbee, so the first Z-Wave LR mesh was installed, and then fortified, and now includes a number of Zooz relays. One group of Zigbee outlets in one room also proved unreliable, and are now my first incursion into Matter (and working flawlessly).
Like others here, I've avoided Wi-Fi and outsider-app-required devices whenever possible (local homogeneous control being the whole point of Hubitat for me). We're currently very happy with the way everything's come together, using each different networking standard for the things it's best at.
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