Cybernetic eyes are harder to make. Doktor couldn't finish making one before Raiden went out to hunt for desperado.The eyepatch he's wearing also acts as an eye without the look of one. Raiden also said he didn't care about his appearance. You should listen to the codec conversations some of them are really interesting and educational.

Just an FYI, that's his LEFT EYE that he's missing.

[url=http://metalgear.wikia.com/wiki/Raiden#Custom_cyborg_body]Metal Gear wiki:[/url] [quote]Raiden was originally supposed to get a completely cybernetic eye to replace the one he lost, but Doktor was unable to create it before the surgery, so he had to wear a makeshift eyepatch for a while.[/quote]