That was a nice ending.

> I was thinking something along the lines of when it's Shinji's turn to commit seppuku, he just laughs at the already disemboweled Rei and Asuka, before Gendo walks in, with two Rei clones, or something along those lines. I actually really liked Gendo's character in Evangelion. Really determined to get what he wanted, and in getting what he thought was best for humanity.
So are you going with the JSSDF scenario, or something different? Cause in JSSDF scenario Rei clones have all been destroyed before, and Gendo is most probably shot on sight with the rest of the NERV staff. And even if it's some other scenario, if you ask me, including Rei's clones in the story only diminishes the finiteness of Rei's death. Also, what's with Shinji laughing at disemboweled girls? That sounds just rude. Let him admire them. Admire the show and admire the girl's resolve to do it.
I know I'm already complaining before you've even written the story, but the things you say just don't sound right to me.