I agree, there is some magic to NGE that RahXephon doesn't have - but I'm not sure how much of that is caused by the fact that I saw NGE first and it was the first Anime I ever watched. I love Neuromancer, but much of my love for it comes from the fact that it was the first science fiction novel I ever read. I had no antibodies. If I had read Vinge first, it's likely I wouldn't have been too impressed with Neuromancer, which has as many flaws as NGE.

I can't justify giving NGE a higher score for the reasons you described, but I do slightly prefer it - though less so after re-watching RahXephon.