USB was available on wintel machines, but hardly anyone used it...
I had a pentium pro and a socket 7 motherboard both with onboard USB, where the ports were exposed as a header on the motherboard and the manufacturers of the machines never even bothered connecting them to actual sockets on the outside of the case. Serial, Parallel, PS/2 and AT keyboards were still common and thats what people used.
Linux support for USB was poor, Windows support for USB was poor, very few peripherals used it and those that did were generally niche as most people bought non-usb versions instead.
It's not until Apple came out with machines that *only* had usb, that people started using it and third parties really started producing USB peripherals. If you leave the legacy ports in place, people will continue to use them because its easier and cheaper to do so. Only by removing the legacy ports do you force people to use their modern replacements.