Eh, I can't say it annoys me... It's like NJO.
I like probably 50% of NJO, and hate the other 50%.
I like Luke's story re-establishing the Jedi, and how all these force-sensitives existed and he's gathered them up (some were soldiers in the war even, like Kyle Katarn, Keyan Farlander... Others were found and exploited, like Maarek Steele and Mara Jade) to train them properly and stuff...
Other stuff I thought was lame, like the Yuzahn Vong's blatant rip-off of Star Trek aliens that were around at basically the same time, and offing Chewbacca as a publicity stunt. So, basically, I just sorta ignore what I dislike and embrace what I enjoyed... Lucas has so thoroughly screwed things up to me, in terms of Star Wars, that I figure he's no better than Timmothy Zahn, a Lucasarts game's storyline, or the latest Darkhorse series. *shrugs*
If it doesn't fit I either try to think of a logical reason it could fit, or I just ignore it. That goes for Clone wars too. I like some of the EU storylines that were out better than what the toon put out that contradicted them. It is what it is.