Skype is actually pretty good for teams. I used to work at a company where it was our primary medium of communication, and we were almost forty people. It's extremely easy to create a group chat in Skype and destroy it with IRC OPs like features. It is also tempting to use since Skype provides a way to initiate a voice call right there from the chat. And one can always access the chat history as well. People have also written Skype bots.

You're right. So what?

There are many businesses that still use Excel as their CRM software, even though there are purpose-built apps that work better.

My point is that Slack, Hipchat, and others are specifically targeting businesses. Having an API with integrations to other software (CRMs, issue trackers, PM, etc.) is one huge advantage over Skype, just as an example.