Porcupine is right. Still, I think that even if Rei and Shinji didn't become a couple, it seems like they could learn alot from each other. Those two seem to have a knack for wanting to die or run away.
It's LIFE, you don't figure it out, you just get one the damned beast and RIDE.
There was no way Shinji was gay - No evidence in the show to support it. The Kaowru thing may seem homosexual in nature, but there's a lot of evidence that says otherwise (Ask me to explain if you wish to know how I think ^^)
Also, I thought the (End of) Evangelion ending was great. The show never did have a happier light hearted theme, it had a very angsty and depressing one; The ending didn't do a 180 and end "happily", but instead ended "realistically". EoE Spoilers Ahead!!...
Humanity screwed themselves over with the Third Impact, and it wasn't going to be stopped. There could be the "No Third Impact, Shinji is a hero, Asuka isn't a bitch, Rei finds her own soul" bunch of garbage ending, but that's not what Evangelion was. The ending, albeit not perfect, was pretty good considering it stuck with the what the show was trying to say. I'm sure we've all seen animes with the good ol complete reverse ending, and god knows at least I myself hate those endings. So, all in all, Eva had a fine ending by my account ^_^.