Threaded replies does seem nice to have, but not nice enough that I'd be willing to give up on the other features of IRC.
One thing that'd be nice to have with IRC is if there were a cheap host somewhere that easily let people run their own weechat instance; too many of the people I talk with keep disconnecting because they don't have / can't be bothered with having their own server with a bouncer. (There's stuff like http://blinkenshell.org/wiki/Start but I was thinking something that one can recommend to complete newbies.)
The interesting thing about IRC is that it can be modified to suit any individual's taste. But, that takes time and expertise. That guarantees IRC will stay within a niche audience of people technical enough to bend it to their will. What I'm liking about these new chat systems is it has some of the best features of IRC made available to all users with an interface they can understand and use.