When I saw Fafner in fansubs a few years back, it didn't impress me. It was yet another Evangelion/Rahxephon clone with a horribly confusing mass of in-media-res unexplained technobabble & a swarm of interchangeable characters made indistinguishable by a particularly poor implementation of Hisashi Hirai's usual polished but identical character designs. I only got about five or six episodes in before giving it up as impenetrable and gnostic. Despite all that, I bought the Geneon DVDs in a recent 25-for-$100 sale anyways. I just got around to watching them.
Boy, did *that* show improve wildly in the second half. The first half's a terrible slog, full of difficult-to-understand characters & outright unlikeable characters. The writing's also kind of slap-dash and unhelpful right up to episode fourteen or so. By that point, however, they've killed off, exiled, or otherwise banished all the annoying characters, and explained the motivations of the confusing characters. More importantly, I think, I could finally remember everybody's names.
Suddenly, everything falls into place, and Fafner goes from dull giant robot knock-off to full-caps AWESOME. The philosophy stops being gnomic, and settles into a thoughtful, non-denominational Shinto vs. nihilistic Buddhist groove. Deaths and battles stop being pointless, and gain resonance and tragic depth. Everybody takes a level in charisma, and the token chick suddenly turns into a cold-blooded godlike sniping killing machine. The Girl in a Box climbs out of her box and turns into a Card-Carrying Deity - to the point that there's an objection during a court-martial that "you can't let God testify in court!' She has at least three distinct Crowning Moments of Awesome by my count. Tsubaki basically steals the show away from the yaoi-bait protagonists.
Even the ending rocked. Fafner's a classic instance of Growing the Beard.