Gendo also does many fucked up things,
Anyway, one of the main plots of Eva is of Shinji hoping to get something out of Gendo, so they would reconcile and finally be a family again, and lots of the viewers expected that during the time it aired. And then EoE came and all of their hopes were screwed up. (Personally I think Gendo became 100% unforgivable for me after episode 18 but anyway)
But the point I'm trying to make is that while Gendo's fate can be very disappointing to those who were expecting a redemption, it is very realistic. After he saw the plan he spent years on failing catastrophically, was there really any saving point for him? Not that he was doomed from the start, but his insistence on his agenda caused his demise. No him running to Shinji and saying "I'm sorry son, let's start over" would change that (it wouldn't be physically possible anyway considering they were very far from each other but still).
Sure Shinji is also full of flaws, but let's not forget he's 14 with a very fucked up life and full of issues, but the show doesn't carve his faith on stone. However, it does for Gendo, and he represents what Shinji could become if he drowned himself in his own selfish urges.
Return of the Jedi is arguably my favourite SW movie, and while quite admirable it is for Luke still hoping that there's good on Vader for trying to empathize with his lost father figure, it is also a bit innocent. If Vader survived his fight with the Emperor, no doubt the Rebels/New Republic would have his execution as the main goal after they had set up their new government, or at least he would be permanently imprisoned for all the crimes he commited.
Even though it would have been interesting to see him having a change of heart throughout the series, I've got to say his ending is much more satisfying considering all the things he did.