There's no denying that some of the things that came with USB, like mass storage and video cameras, are really useful, but I don't think the same is true of trying to replace PS/2, serial, and parallel ports. E.g. USB keyboards do not support more than 6 simultaneous key presses without needing some special workarounds, while it is not a problem for PS/2 interface. Serial ports are still widely used, especially for working with embedded hardware - a UART makes for an extremely simple terminal interface. Parallel ports are easy to interface to, and essentially provide GPIO capability - you can use one to flash microcontrollers and EEPROMs, e.g. to recover from bad BIOS flashes and other similarly bricked devices ( http://www.fccps.cz/download/adv/frr/spi/msi_spi.html http://write-code.blogspot.ca/2012/08/parallel-port-spi-flas... ) And from my experience trying to install and troubleshoot a USB printer (the problem was driver-related), I'd rather stay with one connected to a parallel port.
Latencies are also much lower and more predicatable than USB because these are dedicated interfaces; there's a community of hobbyists using parallel ports to control CNC machines, and USB<>parallel adapters will not work for that.
My motherboard still has PS/2, parallel, and serial - and 8 USB ports. A little-known fact is that most if not all of the integrated I/O chips ("SuperIO") used on motherboards still have all the legacy port controllers, but the manufacturers don't bother connecting the pins to anything.