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.
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.
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.