Onboard graphics, audio and NICs are perfectly functional and more than enough for most people. Both in work environments and at homes. They've not been in a shitty category for years now. They won't break any records, but they will display websites at high resolution, play clear music, and provide more bandwidth than the link to the internet can handle.
Just look at the number of Lenovo's AIOs (and similar solitons) in offices.
> Full USB-C (or ongoing USB-4) means Thunderbolt which is PCIe.
USB 2 is a fraction of the price. (And power and board space)
But 99% of the rest of us just need things that work and allow us access to good performance.
Then why are there so many audio hats, let alone USB audio dongles used even in the RaspberryPi world?
Don't get me wrong, I still run a discrete GPU for gaming, but for a lot of people onboard GPUs provide a good experience, and often much better power efficiency.
Power. PCIe is a fairly power hungry link. On-die parallel connections are incomparably more efficient.
Special low power links like MIPI PHYs also have their place.
USB is high enough speed that you will get quite a bit of overhead from USB>PCI>memory route, and back.
Audio is a particular pita, network too needs as close, and direct as possible connection to the CPU to get maximum performance.
PCI-e lanes are a limited resource on a CPU and really fast. Dedicating one to a keyboard, for example, is probably inefficient.
I have heard (don't know too much about it) some Intel NICs are able to place network packets right in the CPUs cache for maximum speed, this probably can't be done via PCI-e.