Re: Such as?
Atlassian's products seem to have been designed by people who failed data structures at college and have very limited understanding of what is important for development. E.g., JIRA stresses the absolutely useless distinctions between "epics", stories", "bugs", and "tasks", even though the actual workflow does not depend at all on whether you call it a "bug" or a "task" (a "bug" is a "task", after all). At the same time, the most important relationship - what blocks/depend on what - is almost completely absent. Oh, yes, for each ticket you can see the blocked and the blockers, but the tree view (this is where data structures would come in) of dependencies that is, IMHO, all important is nowhere to be seen.
The JIRA GUI is awful (Confluence is even worse), horribly slow (at least in the cloudy version), and changes all the time. Notifications come to you over email, but the email format is unstable, making it virtually impossible to filter/score/etc. on the receiving end. Moreover, JIRA is completely incapable of parsing incoming mails in any sane way and add them to the comment trail in a human-readable form (to the point that it does not even respect its own markup!). This means that one gets notifications through one interface, but must switch to another interface to react. Search is horrendous (and I am perfectly capable of writing SQL queries). Automation is hardly possible - I blame it on the aforementioned inability to handle incoming emails and lack of any alternative channel.
The best thing I can say about JIRA is that it is certainly better than having nothing at all.
What is better? How about a very popular thing that does all the things that JIRA doesn't, and does them very well indeed - Bugzilla? I'd take that any time - I am stuck with JIRA and Confluence because of someone else's decision at work. I do not intend to initialize a migration for the whole organization. So all that is left for me is using it and I cursing it five days a week.