New users often click "Have a question or comment" when they want to reply to a comment instead of clicking Reply and they start it with @username. I don't use other forums but I believe this may be common among other forums as a way to direct who your message is to. Personally, I like the way CP works in this regard.
Perhaps it would be easy enough to check if the beginning of the comment is @username to then insert the comment as a reply to the most recent top-level comment of that user. Something like that.
There are two kinds of people in the world: those who can extrapolate from incomplete data.
There are only 10 types of people in the world, those who understand binary and those who don't.