This is more than a mild annoyance in the case of faster Thunderbolt devices like eGPUs, especially since, in addition to the 2 PCIe lanes dedicated to the USB ports and a third dedicated to an SD card slot, an additional five lanes are unused.
IIRC there was a reason at one point that Intel insisted on connecting Thunderbolt controllers through the PCH, but I don't understand why they didn't at least use four lanes for one of the M.2 slots. Sure, they may have had to move the SD card slot due to configuration limitations, but in what world is SD card performance more important than NVMe performance?
You have to go out of your way to make Apple's Lightning connector look sensible, but somehow the USB consortium has managed to do it.
USB-C moved those to the much cheaper to replace cable. The little strip in the middle makes cleaning a bit harder but does provide for more longevity. It's s necessary evil in order to have the spring contacts on the plug side as well as not having them exposed to touch.
I think the plug side of USB is pretty well designed. The problem is more with the electrical and signalling side and the marketing of the different versions.