Having read every Star Wars book I admit there were stories in the EU that were kinda weak. The problem of making the NJO non-canon is it not only affects that series but also all the books/comics that follow. Writing in the Star Wars universe is a thankless job. You can never satisfy everyone. People need to just accept it the way it is and stop trying to mold it to their own ideas. Were the Vong a bit of a stretch? Yea, but that doesnt mean the whole series (not trilogy) was garbage. As with most of the EU there are highs and lows. That Black Fleet Crisis had some strange things too. Nobody ever complained. How about Truce at Bakura? Entechment, really? Still it was a good book. Instead of complaining about what should be canon and what shouldn't just be thankfull we have a star wars universe, AND now Lucas can't go around changing the movies every other week.
You know that George Lucas told the writers of NJO about how the Vong was gonna be ? so canon they are indeed.