I've seen Soukyuu No Fafner... twice, because I enjoyed it so much.
It definitely doesn't portray a Christian viewpoint, but it is a very interesting secular story about the search for the meaning of life: Existence vs. Nothingness. It does get pretty confusing in parts... lots of science and lots of names thrown around. But I thought it was well worth the effort. (And the "gold things" are called Festums. They don't really turn you into zombies, but it's kind of a spoiler to say what it does do to you.
)
Yes, it was very "Eva-esque", but I watched Eva and didn't like it nearly as much as SNF, mostly because NONE of the Eva characters were very likeable to me. (Okay, I did like Misao most of the time, and I felt sorry for Shinji until watching the End of Eva, when I detested him.
) However, I really liked many of the characters in Fafner and cared about what happened to them. The character development is much stronger in Fafner, in my opinion. And you get to see the Fafners in action much more than the Evas, which is a plus for a mech lover like me.
As far as the shonen-ai stuff, I think people who WANT to see that will find it. But I didn't read any of the relationships that way.
Fafner is definitely not a cheery series, but it was one of my favorites from last year. It even has my favorite opening and endings of all time... I watched them both for all 26 episodes. The ending changes with the growing sadness for many episodes toward the end of the series... quite beautifully done.
It's pretty late, so I'm a bit too brain-dead to come up with my long list of why I love this show, but if you'd like more details, I'd be more than happy to write more later. (But it sounds like I may be in the definite minority in my enjoyment of this show, so maybe I've said plenty already! hee!
)