Seems funny when I think about games on DOS vs. NES. Most of the time, NES games seemed much better.
Around that time, the PC was rather simplistic and not designed for gaming. Graphics were usually EGA (or worse, CGA), and didn't have any sprite support that other systems in that area liked to use. Sound was a cheap internal speaker that was more annoying, especially with lack of volume control.
It took until the 386/486 era before PCs started becoming strong, but developers around that time still needed to think about less powerful systems as opposed to knowing that each system could at least handle a minimum quality of graphics.
Once PCs became modern - VESA, Soundcards, and breaking 1MB barrier, consoles were mostly in catchup. It took until 2000 before game consoles had an internal hard drive.
At the time, NES didn't seem very limited. IT had plenty of great games that played quite well.
Also around that time, programmers were much more skilled at optimization tricks - and didn't have to worry about the operating system.