STID grows on me every time I watch. Nibiru and it's consequences (albeit the latter were limited) lent credibility to the film. I try not to get too wrapped around the Marcus/Khan motivation axle, although after reading many a post, I do find myself scratching my head a bit.
EDIT: Neither ST09 nor STID have done much in the way of slowing down and explaining things to the audience. I'm okay with that.