Let's see. First computer to ship with USB native? Apple 233MHz iMac - May, 1998. . . one month before Window98 came out with USB support that actually worked.
Rather than remove all legacy ports in favor of USB, leading PC manufacturers took a "wait and see" approach and kept shipping PCs with both USB and legacy ports. In a bold move in 1998, Apple introduced the iMac, the first computer to be completely free of legacy ports. The iMac G5 family today includes USB 2.0 (480 Mbps) ports, and IEEE 1394 (FireWire) ports to handle high-speed applications.However, most of the PCs produced today still include both USB and legacy ports side-by-side. This is in part due to the number of legacy peripherals in the market and the fact that the cost of including a legacy port is relatively low. - The USB Revolution - 3/25/2005
Apple did not switch to the Intel chips so they could run Windows. That is just a minor side effect of the change. Apple changed because IBM had reneged on its promise of 3GHz PowerPC processors and was de-emphasizing Apple in its manufacturing plans, shifting instead to support Sony's and Microsoft's GAme boxes. Besides, my G5 runs WindowsXP in VirtualPC for those times I need it.
What are you talking about re the iPod and compatibility???
I haven't seen a parallel or serial device on store shelves in years. I stopped using my last one years ago when I replaced my parallel Zip 100 drive with a USB Zip 250. Plus, there is a cost to including these -- size. Lack of legacy ports is one reason the Macbooks are so much smaller than their competition.