Gendo's a rotten bastard, but he is opposed to whatever Seele was doing and he did keep Shinji from triggering Instrumentality. I don't think he'll win or be a hero, but he'll be used as a cautionary example to Shinji of what can happen when you selfishly pursue your own desires with no regard for anyone or anything else. Byronic hero at best.
I wouldn't mind seeing another take on this scene, but replacing Dix-Neuf with Unit 01 and Lal'C with Shinji and/or Rei:
Unit 01 is destroyed saving them/the Earth. They accept that being one of the Children was a shitty fate to be dealt, but they were able to meet the important people in their lives as a result, and now they can move on without it. I think that would be a nice ending.
Someday I hope that we'll be reunited if that is what's destined to be. Perhaps we'll discover that elusive bible. And then we will finally be free!