I suppose that makes Darth Revan, Starkiller, and many other characters fan-fiction now, doesn't it?
I don't think Lucasfilm thought it all through when the company declared that all past Star Wars games are now non-canon, I mean, what about the games tied around the films such as Rogue Squadron? Are the events in those games now non-canon making the films themselves non-canon? Do we have to wait for the [i]real[/i] Star Wars films?
Edit: This does give me a great idea for cosplay though :D
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Doesn't really change anything. All those storys are fiction anyway. If in your head you decide that the games really happened, so be it. It's not like its real history, it's a fiction story.