I agree that your fanfic is supposed to be about Gendo. He is afterall the only character to get his second chance. You did flesh out his new motivations and reasons behind them. I just think you need to refocus on Gendo and Shinji. The reactions between Asuka and Gendo in your earlier chapter worked rather well. However, I would like to point out why Evangelion fanfics are popular, everybody hated the first ending, and when the newer ending came out, everybody hated it even worse. Thats why everybody loves a good eva fic,(Higher Learning, Eva-R: Redemption) because even though the main characters all struggle, most find some sort of happiness in the end of the story. If I wanted to see a bad ending where everybody dies i'd just watch NGE again. I think you should stick to your original ideas and outline of the story of a love triangle (or square) and a happy ending.

Oh, and please add the incomplete evafic "The Gods Within" to your Fanfiction Mausoleum-'n-Grill "http://www.geocities.com/the_vault_fortress/GWI.htm" as you should check it out if you never have read it.