Individually they all have a lot of flaws to the point that if they only existed on their own, no one would use them. But features like native support for referencing Jira issues in Confluence and having them auto-update makes companies want to use it.
Part of it, I think, is the development tool version of "nobody ever got fired for buying IBM". It's considered the safe choice. Enterprise-y companies get wooed by all the "Atlassian consultants" floating around out there. The ecosystem is just designed to attract enterprise users.
Fair enough, I agree - they are not that poorly integrated as they are just really poor tools.
Their tools are remarkably slow, with each page both being remarkably JavaScript-heavy and constantly reloading (the two should be mutually exclusive, right?).
They really aren't bad, and have some advantages, but they are not a joy to use.
I am yet to find something that works as good as Atlassian products.