Both Kirito and Link are powerful swordsman who have unique traits, given to them by the creators of their world, which marks then as the hero. They both have a love interest in a powerful, and important, rapier user (well most links do).
In most games Link is a different version of "The hero" in a changed version of hyrule. This can also be said for Kirito because when he enters a new game his avatar is different and all VRMMOs in SAO are based off the cardinal system, so it could be sarus they are modified versions of the same world.
The similarities are especially apparent in the second story arc of SAO, [i]fairy dance[/i]. Let's go over the plot of this, and the basics of a LoZ game. A changed Link/Kirito must save Zelda/Asuna from an evil "king", who wants to use Zelda's/Asuna's power to take control of the world. Link/Kirito must journey through an altered version of the worlds they were in before, with the help of a slightly annoying fairy.
There are a few other minor things. Occasionally Kirito will do a motion with his sword which is one of Link's taunts from smash bros. They both have a classic color, and are both made in Japan.[spoiler]should this go in #gaming? [/spoiler]
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SAO Abridged > SAO