I think..this goes into that whole comfort zone we have with Star Wars, A lot of the EU took a brave step and took us out of that zone, and thrusted us into a era of new ideas, and epicness most of us weren't ready for. (Specially with the Vong) I don't know why people are so scared to accept "Force Dead" things when Medichlorians are barely understandable. Tiny aliens and what not. But with the EU being (understandably) more part of Chaos then most are willing to accept, factions, weapons, force powers, its more part of Chaos than I think we believe.
Yes we have our own lore, but the original lore builds up to this in a sense. The EU is important cause we take it, and we build off it to make lore here. Will it effect my writing? No Revan is still canon, Dark Jedi are still canon, Republic Commandos is still canon, there's plenty of the books that are still canon that I enjoyed, granted Legacy of the Force isn't anymore...damn them!!!