Headcanon - Kaworu is a young clone of Kaji
This is a "theory" that I've been playing with. I haven't done the math, or deep dive into where / when Kaji was doing into order to make it make sense.
I think it's a bit odd that we KNOW that Rei is a clone of Shinji's mom, but Kaworu seems to be the same type of half-angel Clone as Ayanami, yet the franchise makes no allusions to who provided the human side of his DNA.
The only thing I'm basing this on is that both Kaji and Kaworu were kind to Shinji. But, in addition, there's only a few dead characters in Evangelion (Shinji's Mom, Asuka's Mom, Ritsuko's Mom), but Kaji's the only dead MAN.
The problem with this as a "theory" is that Kaji and Kaworu don't look too similar. Rei actually looks a lot like Yui Ikari, while Kaworu doesn't match Kaji's hairstyle. But, I think it's fitting that these dead characters come back as Angels.
Oh, wait, there's also Misato's Dad... what does he look like?
What the deuce?!?!?