But Star Wars is not Marvel Comics. Big difference. Most notedly, the Star Wars movies came before the EU, not the other way around. The EU is essentially liscensed fan fiction. Well done, interesting stories, but they preceed the source material and are not created by the original creator, making those stories inferior and less relevant to the movies.
You will understand better when the new movies come out and don't match at all with EU. Remember, Lucas wrote the outlines for 7,8, and 9, probally ten years before the majority of the EU was ever conceived.
So its not Lucas borrowing from other authors and adding his own touches like they do with marvel films. Not to mention that the story telling of Star Wars is more realistic, linear, and concrete. Comics have varied timelines, realities, human heros that don't age for 50 years, things like that. So you are attempting to compare unequal things.
While the EU can be considered separate canon if you will, the movies have always been the primary canon as decided by its creator and acknowleged by most fans.