Going with the SW canon will make the developer's storywriting problem a helluva lot easier, as now they only have to write according to one background and not 16. Of course, there should still be multiple endings for K3, and there will most likely be a canon ending that will be used for reference in future SW works (assuming K3 wraps up the videogame portion of the franchise).
Command & Conquer was known for having multiple endings, but only the canon ending became the basis for the next game, and (IIRC) the fans accepted that.
Besides, you want DSF Revan for K3? Make some mods once it comes out
Oh yeah, and I hope K3 has at least one makeout scene in it. One we actually see.