You may want to check out the rapidly growing number of RPi clones... cheaper and often more powerful, besides still having GPIO pins. You can find a nice list of options on the Armbian download page: https://www.armbian.com/download/
There's a lot of clones, which is a good thing, but they are kind of a mixed bag on software support.
The one advantage of the Raspberry Pi is it's the one with the most of everything. Other noble competitors, like the Beagle, are pretty good too but getting anything to run on them can be really frustrating.
It gets even worse when you buy really expensive SBCs from random small companies. You want support? They just ignore any emails because they either can't read your language, closed up shop, or just don't care to respond. Only good thing is that at least the hardware is amd64 and it uses drivers that are in the kernel.
I've seen USB GPIO breakouts, but not very cheaply, and I suspect driver support might be an issue. Certainly controlling GPIOs via /sys is extremely convenient! Between that and the built-in Ethernet interface, I suspect a Raspberry Pi makes a better GPIO interface for a PC than almost anything else on the market.
Really ? Because this is trivial to make using a microcontroller. Or you can use any FT232 serial interface.
I mean I'd think you'd prefer an arduino for this application over pretty much everything else since you can quickly upload small programs to the arduino that keep the "fast" logic on the arduino.
Arduinos cost more than a lot of Pis, though. And the network interface of a Pi enables some really interesting capabilities that don't exist, or are harder to obtain, with a device that doesn't have one.
I think ESP8266 boards (running something NodeMCU) are becoming the more popular replacements for Arduino. They're super cheap, and have integrated Wifi.
Cool thing about them is that you can write in C-like AVR code (like Arduino), or micro versions of Lua, Python, and other choices.
4 dollars, including shipping. At this price, they're pretty much disposable. Pi's seem to have bad shipping costs, so they're 20$/piece for the cheapest:
14 GPIO (although with hacks you can do more), including 10 bit DACs on all of them, and 4 with hardware PWM. Most have alternate functions, like I2C, that can be used.