I am looking at building a new PC, and I came across this question myself. Recently, some motherboard manufacturers have announced support for Thunderbolt 3. And what's not to love about it? Very high speed and backward- (or is it sideways-?) compatible with USB 3.1.
The issue is that you can't get everything you might want on one motherboard. The Intel Z170 chipset found with the TB3 Alpine Ridge controller has a limited number of PCI Express lanes for IO. It's 26 to be precise, 6 of which are basically reserved for USB 3.0 and interconnects, so 20 usable. So these 20 lanes have to be divvied up between PCIe slots, storage (including SATA and PCIe-based storage like m.2 and u.2), networking, Thunderbolt controllers, USB 3.1 controllers, etc. (Graphics cards still use the separate 16 lanes provided by the CPU.)
The Alpine Ridge Thunderbolt 3 controller takes up 4 PCIe lanes, which would only be ~32Gbps of the advertised 40Gbps, but it also hijacks the Display Port interconnect from the CPU to make up the difference. This is why I doubt we will ever see full-speed Thunderbolt 3 PCIe x4 cards. To get full speed, it will have to go in an x8 slot and split bandwidth with the GPU, as chipset PCIe lanes are only in x4 groupings.
So to get TB3, you will have to give up something... like an m.2 slot or 4 SATA ports or that 3rd or 4th (Crossfire) GPU or just an extra PCIex4 slot. But the question is whether it's worth trading towards. So, I looked at the proposed uses for Thunderbolt 3 through the lens of an enthusiast PC user and detailed my observations below. Note that these use cases could go quite differently for mobile or small form factor users. In fact the use as a docking station port for laptops is very compelling.
External Storage
This is perhaps the most likely enthusiast use of TB3. However, I see this only being used in specific cases where storage is a bottleneck (video content creation, for example). I don't see this being used by an average geek like me. My storage server is (would be) mainly for centralization purposes with large capacity disks. So, it doesn't make sense to build a new PC with TB3 for this purpose. I build the new PC for use as my workstation, then put the old one on storage duty. So my storage server isn't going to have TB3 anytime soon. Even if the old computer had it, I don't need to buy an external TB3 enclosure when my old computer has connections and room for drives internally.
Displays
This use case is not interesting for a desktop enthusiast/gaming PC. Monitors are plugged into dedicated graphics cards. These tend to directly shove pixels out to displays themselves for maximum performance. I can't imagine a graphics card mfg who wants to route their output through a Thunderbolt controller for output (risking performance), when they could send it to the display directly. It could be that graphics cards will eventually have TB3 video ports, but that's not anything I need to have on my motherboard.
Device Charging
Only for mobile scenarios. I don't have a pressing need for this feature when wall sockets still exist and are in more rooms than my computer.
USB3.1 (Gen2) compatibility
This is nice, but type C USB connectors are already present on most current-generation motherboards without TB3 for less IO budget.
External graphics
This is really only useful for mobile scenarios. My desktop already has a place set for a video card or two.
Thunderbolt Networking
The "for-free" scenario mentioned in press release was connecting 2 computers with a TB3 cable. That could be interesting for transferring data in limited scenarios (e.g. support), but will require software to make it work and TB3 becoming ubiquitous to make it even remotely likely. Using TB3 to hook into a larger network is far from "for-free". You'll likely buy a TB3 to RJ45 converter in that case. Your other option would be a switch with a TB3 connector, which is made less likely by the fact that TB3 cables top out at about 3m or 10ft. Increased distance optical TB3 cables could be a thing in the future, but will likely be much more expensive than an adapter + CAT6 cable.
In all, I don't imagine myself ever using Thunderbolt 3 from my desktop PC, so despite my initial inclination, I'm not going to aim for it when building a new PC. However, I will look for it on my wife's next laptop.
