Interesting. I find that the final few episodes of Evangelion are the ones I appreciate the most. Some things you need to understand about the series:
1. You *MUST* watch the series more than once to understand most things. My friends and I had 3, 13-hour “Eva-thons” followed by lengthy discussions about all the various religious symbolism. These sessions really helped us appreciate all the small nuances that were placed throughout the series.
2. Sometime in the middle, Hideki Anno (The director, who interestingly enough directed “Kareshi Kanojo no Jijyo” aka “His and Her Circumstances”) had a mental breakdown. I'm not sure of the reasons, but it's the episode where Rei has this giant exposition and you see a whole line of them. He started to re-evaluate the meaning of life from his personal view, and that is partially why there was such a huge shift in focus FROM mecha-battle orientation TO philosophical beauty.
3. Evangelion was meant to address all the crap other mecah shows (like Gundam) are about. Some in Japan viewed Eva as the antithesis to those shows.
4. Ultimately, the series is a "Coming of Age Story." My take on the final message - "Don't get tied up with only identifier (ie. sports, a person, an ideology) because if you should lose that identifier, you lose yourself," “You must love yourself before others will you,” “The only person who can understand you and take care of you in the end, is you – so *you* must take care of yourself.”
In the end, Eva isn't for everyone. It's very much a love/hate relationship. If you want your standard Mecha Show, stick to Gundam and the first half of Eva. If you want a more intellectually challenging series with some message, understand the last half. Then watch End of Evangelion and have your mind blown to hell.
BTW, here are some helpful links to understand various references in Eva:
http://mywebpages.comcast.net/juzzam1/NGERCB.htm
http://www.evangelion.ca/rcb.html
I'm open for discussion on the series - it's been a while since I had a good Eva Debate.