It's true that this is a common theme in Evangelion, but Hideki Anno explicitly rejects this sort of thinking. The whole message of Evangelion is to accept yourself as an individual, with flaws, and to work to change and better yourself with other people, and to form real relationships with them. As is clear from the show, Instrumentality isn't a natural thing. It's not a religious reward. It's fool's gold. Rather than real happiness pursued with other real people, you simply lose all individuality. What's another way of saying you become one with the universe? You die and return to dust. That's all the people who remained in Instrumentality did. To be happy, you must first be, and you qua you cannot be unless you exist as an individual. Otherwise, there's an amorphous blob of happiness, maybe, but it's no better than suicide as you, the self, are gone.

The trouble with this interpretation is that it's horribly pessimistic and the ending of Evangelion is canonically optimistic. The real ending of Evangelion is the end of the TV series with the "congratulations" given to Shinji for him realizing he can grow and be better. The whole point of the show, as Hideki Anno has said is for people to learn that they can grow to be better, and they don't have to turn to escapism (e.g. watching mecha animes for his otaku audience) to avoid their problems (he has spoken about how he did this himself and escaped depression by learning to stop being an otaku and to actually embrace reality and life). Instrumentality is the ultimate form of running away from your human problems.

The main point you seem to be missing is that Instrumentality isn't a good thing. It's inhuman, and the desire to pursue it is driven by insecurity and loss, e.g. with Gendo Ikari losing his wife. When everyone turns to goo, we see how in their last moments, Rei turns into whatever the people she was killing were pining for, but never pursuing. It's artificial, fake happiness rather than the true happiness that comes from accepting yourself, learning to be better, and pursuing your goals with real others (despite the Hedgehog's Dilemma).

Ultimately, I guess, I defer to the directorial intent of Hideki Anno in interpreting Evangelion, a show/movie that is otherwise pretty difficult to interpret, especially without a decent amount of life experience.