It's just not easily translatable. I think "like" works because you can interpret it as "like-like', but it also encompass a lot more, since Kaworu does include that angle of godly affection as he is (probably) not fully aware of human emotions, which is what allows him to just immediately reach Shinji and bring down his defense mechanisms, because he doesn't even know these exists. Suki in this case does have a stronger meaning, but it's also very possibly simply more intimate - again, Kaworu has no consideration for "personal spaces", which is even more shocking to a Japanese person. The whole line, and other lines preceding it, are deliberately ambiguous.

It also encompasses the other layers of Kaworu's character like his motherly associations - which go in line with the pervasive Freudianism of the show and Shinji developing to "get out of the womb". Which is why you have the "koui" as well, and Shinji's uncertainty. Literally, Shinji could even say "I guess, I was fond of him", because his character at this point is making interpretations of his own of what Kaworu says but doesn't fully comprehend.