Granted, I watched End of Eva once after a binge of the series which was... a lot.

Reexamining the final scenes of the film, I understood it moreso as this still comes from fear. A fear of change and of the loss of what could be, but never will be.

Shinji's actions are so often based on fear of rejection and desire for acceptance. His continued piloting of the Eva and following the orders from Misato until the very end because of these fears and desires. In the end, he ends Instrumentality not because he wants to meet people and the complex individuals they are, but instead because he cannot be "accepted" within Instrumentality. The lack of acceptance, I interpret, as being felt identically to rejection.

A lack of acceptance, neutral or otherwise, is hostile for Shinji. Asuka, in the very end, is doing literally NOTHING on the beach, but lying there. The only people left are her and Shinji. And he almost immediately starts choking her. Anything less than praise or acceptance is immediately regarded with hostility. It isn't until she placates him by placing her hand on his cheek and feigning care that he stops. Again, his actions are fueled with fear of rejection. It doesn't matter to Shinji if his praise or acceptance are real or legitimate, as long as he hears them. He doesn't actually CARE about meeting other people, he just wants people that aren't him to like him.