First of all, Kaworu is not obsessed with Shinji’s happiness in a yandere way. What happens is simply that Kaworu was trying to find his happiness through finding Shinji’s happiness. He wasn’t selfish and no one ever says this word in the script, on the contrary, he was too selfless because he kept dying over and over for Shinji and that left Shinji catatonic and wanting to die too as happens in the first hour of the new movie. Shinji keeps getting flashbacks to Kaworu’s death and is reminded of this everytime he sees Asuka wearing the DSS choker. He vomits everytime and refuses to eat or drink. He’s letting himself die here, and doing it in a slow painful way because he thinks he should have died instead of Kaworu.

Rebuild Shinji and Kaworu, in this universe, turn out to be NGE Shinji and Kaworu, they already said they loved eachother in the anime, so their love is still here in Rebuild. Kaworu remembers every time they met and Shinji gets his past memories.

Kaworu tried over and over, because he loved Shinji and made Shinji the focus of his purpose in life and happiness, to meet him over and over everytime a loop happened.

Shinji appreciates this obviously because he loves Kaworu too as he said in NGE, but this is not his happiness and Kaworu misunderstood, because Kaworu dying and suffering is something Shinji doesn’t want.

Shinji compares him to Gendo, as in that he made him and only him the focus of his life just like Gendo made Yui and only Yui the focus of his life. There are other parallels here to Kaworu. A connection to Gendo playing the piano and being lonely until he fell in love with Yui. This comparison is also one to Shinji and Kaworu’s love being real.

It’s said that Kaworu chose Shinji because he never changed no matter what, but at the same time, Qworu was able to form connections with others, in this case, with Kaji since they both were working to stop Seele/Nerv and worked for  Wille together, and having experienced that, at the same time, he’s glad that Shinji changed. Kaworu secretly wanted change too. He wants to be free too because he too is aware that no matter what he can’t escape his fate, but he’s powerless, there’s nothing he can do.

Shinji realizes that nor Kaworu nor anyone here is is control of the Eva world, and that the loops just happen and that as long as Kaworu is an angel/Adam he’ll be forced to repeat over and over and suffer over and over.

This goes for Rei too. The Eva world can’t be changed, it’s doomed to end in tragedy every time. As long as this Eva world exists, Kaworu and Shinji can’t be happy.

He talks with both Rei and Asuka separately and has closure with them and their relationship too.

In their instrumentality sequence, Shinji and Kaworu met in the same beach of ep 24 and say goodbye while Shinji (as a kid) holds Kaworu’s hands and Kaworu cries tears of happiness.

In the end, while Shinji and Kaworu loved eachother, sadly, they would never be able to be happy in a world with Evas, because as I said, that world will always end in tragedy. This doesn’t invalidate their love and it doesn’t invalidate the nice cute and canon moments they shared in NGE and 3.0

As true star-crossed lovers, the universe is the real problem in this relationship. It’s outside forces what stops them from being together.

Since the universe is what is making Kaworu (and everyone else but we’ll focus on Kaworu) suffer, Shinji creates a new world where Evas don't exist so he can be free.

In this new world Shinji wears the DSS choker, that before gave him ptsd, to pay for his sins and the sins of his father. He waits years, more than 14, waiting just like Kaworu waited for him, to see with his own eyes if Kaworu made it to the new world and if he’s happy (Kaworu died for good in 3.0, Shinji talks to his soul in instrumentality and all that so he’s waiting to confirm that he was reborn as human). Shinji, now being like 30 to 40 years old, sees a young adult Kaworu (talking to Rei but the focus in on Kaworu smiling) and finally smiles after so long. Mari appears and takes the DSS choker from him. Now that Shinji knows that Kaworu (Rei too) is happy and free from the loops and his horrible fate, he allows himself to move on. He and Mari turn around and leave (the scene implies this new world is our real world where Evas don’t exist)

I still have problems with this movie, but don’t panic and say that KawoShin is destroyed or non existent. They just couldn’t be together because of stuff that wasn’t in their control.

Here you can choose to do one of two things:

You can believe that now in this new world without Evangelion, without loops and all that, Shinji and Kaworu, maybe not now because Shinji’s older and stays with Mari, but in the future once they are reborn once more after this, that they’ll find each other again and now, with no universe or pre destined fate  ruining everything, they’ll be happy together, be it as friends or lovers.

Or

You can accept this story is over and move on from Evangelion. Appreciate it for what it is and appreciate the conclusion. Or you may not like the conclusion or aspects of it or the movie, that’s ok too.