Frankly, I'm a little surprised at the hate for the couple thousand or so transistors required to support the set of 8253/8259/8250/8042/etc chips that form the basis of the original XT/AT. Especially given the love for all things ARM, which tend to implement their peripherals in a very 1980's way with simple fixed MMIO ports punched into the address map, but without the standardization that form the basis of PC/AT hardware.
And just to stay on topic, almost every single decent ATX/ITX board I've used in the last decade has a 4 pin PC speaker port. Including the skylake machine I built last night. Same thing goes for RS232 ports, which are still on the vast majority of decent PC hardware even if they don't have headers soldered on. The X99 in that review actually had the headers, and I owning the older version of the board actually have a cable plugged into it which I attach to assorted hardware for firmware/etc work.
Isn't that a source of flexibility, though? The fact that that stuff is not standardized and is instead hidden behind a hardware abstraction layer (the OS kernel) means that ARM systems get the freedom to drop the legacy interfaces and centralize the hardware abstraction where it belongs: in the kernel.
However, for that you need:
1) a specific kernel for specific hardware, there's no universal kernel like for PC and
2) lot of hope that the maintenance or support of that specific kernel is not going to be dropped as soon as the hardware ships out of the gates (which is the fate of many routers or android phones, which cannot be updated to newer OS releases).
As someone who works on embedded systems, the serial port is really useful for debugging when nothing else works.
In a modern PC, almost none of these are used - why would anyone want to use the crummy old AT 24-bit DMA controller when you can use PCIe bus mastering - but they're there if want to boot into an old real-mode OS.
The beeper using ancient interface is also long gone. Nowadays, the HDA chip handles it most of the time. There is no reason except ancient compatibility to call into the beeper via the ancient interface.
j/k... but I hope a Hero Will Rise
[1] https://www.amazon.com/SANOXY-PS2-Keyboard-USB-Adapter/dp/B0...
The motherboards that do come with PS/2 usually implement their chipset.
Also PS/2 stopped being electrically compatible a while ago around about the same time that the combo Keyboard/Mouse PS/2 ports became available.
It offers pretty low current only about 250ma so you might have issues with older AT keyboards even if the chipset is still AT command compatible.
For Intel system super I/O was eaten by the ICH which initially kept compatibility with most Super I/O functions.
By ICH 6 or 7 which is around the mid 2000's most of those legacy features were all gone.
By 2008-9 the ICH was also gone and replaced by the PCH which doesn't have almost any compatibility or features with the Super I/O architecture.