Why can't you @reply more than one user? It seems like I should be able to @reply at least two users. I've run into this problem several times now. Is there a reason why you can only @reply one user?
This would be useful on occasion, I can't deny...
But the rationale is simply that comments aren't meant for tangential discussion. The author of the post you're commenting on is always notified, regardless of whether he's "@-replied" to explicitly in a comment. Responding to one of these comments requires only a single @-reply. Allowing comments to notify multiple people could result in obnoxious behavior or harassment.
As Diago notes, this has been discussed several times over on MetaSO - this is a good example.
It's worth contrasting the design of comment @-notifications with those of chat, where you can notify multiple users in a single message:
In short, chat messages will only notify people who are probably expecting them, having recently joined a chat room for the purpose of chatting. Comments might notify people who've long ago forgotten about the topic. Making it easier to mass-notify multiple users via comments has a much larger "harassment" potential.
From this Meta SO answer
It contains most of the details behind the system, however the short answer is that it is related to the lack of display names, and it was really a system put in place as an afterthought, since it is not a defining feature of SE.