I like the show and movie a lot. Among my favorite anime if not my favorite of all time and among my favorite stories in all media. Upon my first viewing, I didn't think they made zero sense, but I had a feeling some of my thoughts might be wrong. I've also watched the rebuilds which are more divisive and I think deserve to be. However, "the curse of Eva" (a video essay on youtube) does a good job explaining those movies. When I first watched them I thought the Red Sea was suppose to be a sequel to the original and was super confused (and didn't really like it), but 3.33 is my favorite now and better explains what the movies are about. It's still possible I'll end up disliking the rebuilds if the ending of 3.0+1.0 drastically changes the meaning of End of Eva and the show. Ultimately I still don't view the rebuilds nearly as high as I view the show or End of Eva which I consider masterpieces, but I could love them just as much depending on how it all ends. However, I didn't really need video essays for the original story or end of Eva. I more or less looked into the Eva universe to confirm thoughts and just because I was a fan of the show. I thought they were pretty easy to understand in comparison to the rebuilds.
The writers and director hint at many things throughout the series that the core messages are about overcoming depression, escapism, and moving forward in life despite the nature of life being suffering and misunderstanding. The ending scene depicts Shinji and Asuka overcoming instrumentality and given special privilege from Rei who priorly joins with Lilith and is given god-like power over humanity. Gendo and SEELE's plans both fail because Rei doesn't like them or believe in their goals for humanity. This is hinted at in certain scenes and heavily proven in other/expanded media.
SEELE basically only wanted instrumentality for themselves because they represent the elite or illuminati conspiracy and Gendo wanted to be with Yui and to convince Rei to prevent instrumentality because he represents a god complex. Instead life is rebooting through Asuka and Shinji as they are alive erasing the eugenics that SEELE intended, but instrumentality does begin which means Gendo failed. The council was not placed inside Eva-01 as SEELE wanted, instead it floats into space as an empty vessel.
Rei has grown to see the good in Shinji and Asuka and the negative in Gendo and SEELE. As she chose to link with Lilith on her own terms she is granted god-like power without Gendo or SEELE having any say in the matter. Ultimately Rei chooses to use her power to aid Shinji, Asuka and humanity as a whole in a sense by allowing all of humanity to enter instrumentality and exit it at their own will. She shows sympathy to Gendo and SEELE in this way as they aren't explicitly shown being destroyed or separate from the rest of LCL, but their power is completely eliminated from their intended goals.
The way I interpret the ending is through combining the show and movie ending. Shinji rejected instrumentality. This is somehow still a debate among fans which blows my mind. I thought this was the case upon first viewing of the show and movie, but it's explicitly stated in text via the manga if people are still skeptical about that.
For what happens after is up to interpretation. Now someone might say the feeling of the end of the show and end of Eva are totally different because of Asuka and Shinji vs the clapping scene. I view the clapping scene more or less being a spiritual thing that happens before Shinji comes back to life. However, even after Shinji comes back in a better state he's still human after all and I actually assume the scene we see in End of Eva not as directly after Shinji comes back to life, but some time after resting. I remember reading an alternative version of Eva which elaborated on the graves we see. It stated that Shinji made them and Asuka kicking over hers when she comes back to life. So some time has passed since Shinji originally woke up from instrumentality and Shinji seeing Asuka alive is shocked and surprised.
I stated that Shinji grew and escaped instrumentality and yet he chokes her? Well why would he do that if he grew as a person? He chokes her because he's still not fully overcome instrumentality in a sense and this scene is actually the final climax. There's many possibilities for why he is choking her and they aren't necessarily mutually exclusive. Maybe he thought she was dead from the mass production units or that's he's going crazy. He just can't believe she would choose to leave instrumentality for him. I've always viewed them as meant for each other so to me it all added up as an inverse tragedy that was meant to be overcome. I view the ending as a good ending and that Asuka and Shinji will survive this post-apocalypse hellscape. As for how they eat and survive well that would require a sequel to flesh out the details, but the movie poster shows they are both okay in a scene that takes place after the choking scene and given Rei's godlike powers I think it was already foreseen and planned for. I love end of Eva and compared to all the nihilistic media out there I think Eva actually flips into something beautiful and hopeful.
/I might edit this later for typos or clarification. I just sort of ranted this out without much proofreading.
