I'm sure are features IRC cannot duplicate, but all that's necessary for that is a bouncer.
And sure, a bouncer with some plugins could do it, but you'd have to set it all up. I've had "have bouncer email me when I'm mentioned in a channel" as a mental to-do for the past five years, and it's never been a high-enough priority for me to sit down and expend the minimum of two hours it would take (and likely much more.)
And, most importantly: I don't have to manage the damned server ;)
But we have shit to build! :)
We have a jira integration set up and every ticket consumes five lines plus plenty of whitespace - a few of those and there's no real comms visible on the page. Every integration I've see consumes gobs of space. Similarly, flagging announcements by assigning a colour is almost worthless - the colour bar isn't very visible (I prefer hipchat's method, where the entire chatline gets the background colour set). Then there's the problem of people's actual chat messages being the least visible thing on the page - smaller and less noticable than names, integration notifications, what have you. But the onboarding is so easy, it just sucks users up.
Being able to see a conversation instead of bells and whistles? I miss that... but plain text scares regular users...