Okay, thanks for the replies. Here are a few differences I've noticed, might be enough to cover me up:

-The actual war between aliens and humans is happening in the background, the main characters are juist a couple of smalltown kids who spend most of their time running away.

-Also, there's no real equivilent to NERV - the aliens are being fought off by, simply enough, the military.

-Neither side has huge, manually-controlled cyborgs.

-From what I understand, the symbolism in Eva is mainly for the viewer - none of the characters say "hey, what's with all the Judeo-Christian imagery?". In Rust, it doesn't tak elong for the aliens' naming pattern to be noticed, and there's a lot of speculation on exactly how they got those names.

-Also, the mythical names are restricted to the aliens, unlike Eva, which has plenty of religious names on mboth sides. So, the military won't, say, create a weapon with a name like "Titan" or "Ragnarok".