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Next you'd be asking why vampires dust with their clothes when staked, or why the mayor wanted to be a big snake, or how the untrained Xander never got killed on 7 years of patrols, and then the entire 'verse would collapse on itself!
The magical and the mystical don't tend to mix. It's true that Dark Willow brought Buffy back with powerful magics but a bullet wound isn't the same as having your eye gouged out.
Eyes are a complex and fragile biological mechanism and I just don't see magic as that subtle a tool, at least from what we're show, to be able to repair Xander's disability.
But...he could always get a bionic eye! That would be cool!
It could look like a normal eye (or maybe not) but have additional cool gadgets built-in; X-Ray vision, lasers, microscopic mode, I-Pod, etc.
Because from what we see the technology certainly exists (the various bots for example, Adam for another), they could rebuild him...
Hey, I figured out a use for Andrew!
Well, remember, Xander is "the one who sees everything." Maybe they could use that to finally give him his own special power. Willow could give him a mystical "All Seeing Eye." that could have a lot of potential for future story lines.
Of course, that would mean that they would have to designate someone else to go and get the doughnuts...
I guess they simply wanted to have the Nick Fury/Xander parallel and it his an visual symbol for what he had gone through.
S03-06 Willow had fixed his eye (assumed she had the power) most likely without his consent to make him happy resulting in Giles and Tara scowling at her because of the Violence Against Nature ignoring that Xander Is More Likely To Survive In Battle With Both Eyes. Xander would be angry at first because of the consent part and because he doesn't like others to fix his problems. It makes him feel vulnerable. But when he came around he would thank her in a sappy, cute Xillow friendship-y fashion. <3
S07 Willow was too scared of going dark again/The First infecting her again to do any spell at all. She would have done it if he had asked but Xander wouldn't want it anyway for his own but mostly for Willow's sake. Had someone else (Buffy or Dawn) asked her, Xander would have interfered.
S8-10 Willow probably asked him but he refused for above reason AND he came to the conclusion that it's kinda cool, sexy and a lady magnet anyway.
Maybe it's easier for Willow to reanimate a complete, intact corpse (such as Buffy) than it is to rebuild a part of the human body that is long gone? Maybe she needs the part in order for the spell to work?
Plus, like @thetopher said, the human eye is intricate. It might be she's not quite that powerful, or it just can't be done by witchcraft...
Speaking of Xander's eye patch, I wonder if he swapped his allegiance over from DC's Sargent Rock to Marvel's Sargent Nick Fury? He quoted "what Sgt Rock would do" several times during Seasons 4, 5, and 6, but I haven't heard him say "Sgt Nick Fury would..." as of yet. Of course, SGT Nick Fury never had an eye patch. It wasn't until much later, after he left the Army, that he lost his eye.