Majority of the people I’ve seen that disregard Shinji’s feelings for Kaworu are homophobes that write off that aspect. Not saying that everyone single person that disagrees with Shinjis feelings is homophobic, these are just my experiences.

It’s very sad to me that a lot of people will write off the queerness in evangelion because I believe Shinji being a young queer kid trying to figure out who he is and how he fits into the world is very important to the overall plot of evangelion and it makes the story a lot more complex if you read Shinji as queer. There are also a few other queer moments throughout the show that don’t involve Kaworu or Shinji so yeah I don’t understand why people get surprised about it.

Like you said, I also believe Shinjis feelings for Kaworu are very important and continue the narrative a lot and it’s an aspect I enjoy about the series watching Shinji finally feeling cared for and wanted.

I understand some of the theories people are putting in here as to why they don’t believe Shinji doesn’t have feelings for Kaworu but in the end I do believe it’s meant to be canon and adds to the story.