I preferred FMA because it is more up my alley in terms of my taste. NGE was superior in some aspects, but the final handful of episodes were such a turnoff for me that I can't possibly put it above a 7.
Neon Genesis Evangelion is alright. Doesn't really have any glaring flaws. Some people on Infinity bible thump it though. Fullmetal Alchemist is better than it too.