CodfishCartographer posted:

Yeah Yui wanted to be a sign that humanity existed, even long after humanity itself was gone. We don't really know enough about her character to know why this was so important to her, or how she'll feel after a few quintillion years floating in space alone, but we also don't really know what level of consciousness she has in the eva anyways.

It's unclear what happens to Gendo at the end, he's the only person we see still bloodied and non-tanged during instrumentality, so it's fully possible that Shinji explicitly wanted him and him alone to be exempt from the process. However after seeing (what's left of) his corpse, we then see the three Reis standing and watching him - which is what happens before someone gets merged into instrumentality. I think his fate is meant to be deliberately vague and up to the viewer's interpretation. As for his motivations, Yui was seemingly the only person Gendo really connected with, and yeah his plan was basically to start instrumentality solely so he could see her again, and he seemingly didn't give a poo poo if anyone else was cool with instrumentality.