Oh, I definitly agree- I think part of the reason that Leon and Angela seemed vaguely interested in eachother was the fact that Degeneration was written kind of poorly. I couldn't see him getting so attached to Angela is he was in character. At least not without some kind of mention of Ada.
Yeah, I agree with the strong emotional bond between these two. I mean- how many times did they risk their lives for eachother in the second game? Leon took a bullet for Ada, and at the end Ada 'died' to protect Leon. Again, in RE 4, we learn in Separate Ways that Ada was behing the scenes the whole time- at one point going against Wesker's orders to stop Leon's assassination. Also, since we don't really know if Ada's 'good' or 'bad', I think Leon is the one link she has that keeps her attached to her humanity. It's rather evident that Leon and Ada have something going on between them that each of the possible three pairings (Angela, Ashley, and Claire) are missing.