I still don't get why people put Leon and Claire together. Their relationship has been nothing but platonic, and I don't see that changing anytime soon.
I don't really count Angela Miller, particularly because I don't feel her 'relationship' with Leon was well-thought out by Degeneration writers. She was so rediculously cliche, and Leon wasn't really himself either.
This shouldn't come to a surprise, but I definitely think Leon belongs with Ada. I think he has the strongest romantic relationship with her. In RE 4, he made it clear to Ashley that Ada is 'a part of him he can't let go of'. And in the Separate Ways scenerio, it's blatently obvious that Ada still cares deeply for Leon as well- she goes well out of her way to rescue him, despite Wesker's orders. I think he's kind of her last link to humanity, in a way.
So, yes, Leon belongs with Ada.