The PCIe lanes are the worst. You have x16 slots that run x1, you need to check slots with m.2 to make sure an x8 doesn't become x4 if you insert storage. Wait if I plug something into the thunderbolt port my 10g network card runs at half speed? Obviously these are actual physical limitation from PCIe lane counts, but it makes it impossible to search. Just painfull.
My advice to anyone doing motherboard shopping is to read the manual off the manufacture's site before deciding. The pcie lane tradeoffs tend to be in the block diagram next to the contents page.
This is exactly why my comment goes over the head of people who cry just get the basic boards. No, this is why the basic boards for $100 don't cut it. You now need to dive into the technical data and realize that the $100 board seems like a deal for a reason, and suddenly the $300+ category is your only option if you want to get a PC that doesn't run on fake specs.
I'm just struggling to figure out how many people actually need the PCIe lanes for anything more than GPUs and storage, though.
Like, what are you actually connecting your desktop to?
The only reason laptops depend on Thunderbolt is because they have limited internal expansion and need high performance external I/O.
If you need more things than gaming boards offer then obviously you have very advanced needs and can go pay for a workstation board, something like an sTR5 socket Threadripper board.
They exist to partition capability so that enterprises can’t connect all of their peripherals and some ECC memory to get the same functionality for 1/10 the price. It’s not a physical limitation.
Obviously market tiering is part of it and you can play tricks with north and south bridge and pcie switches (which adds cost), but a ryzen board that advertises a pcie 5.0 x16 gpu slot and 5.0 x4 m2 slot only has 4 lanes left to work with from the cpu (i.e the cpus only have 24 usable lanes). Which while you can play with generations to get more lanes it's effectively still 16gb/s. That needs to cover network, extra m2 slots, usbs, as well as the extra PCIe slots.
I don't mind having to work within those physical limits but I do want to be able to search for boards that support N components. i.e 1x 4.0x8, 2x 3.0x8, 4x 5.0x4 . But the best you can search for is physical sizes of pcie slots and then dive into a spec sheet for each one, only to find that the 6 x16 slots only have 1.0x1 of bandwidth each.