As others have said here, the main problem is just that it’s really slow. Apart from that, I think the only item on this list that really puts its finger on a

As others have said here, the main problem is just that it’s really slow. Apart from that, I think the only item on this list that really puts its finger on a key problem is #1, inability to manage dependencies between projects. You try to work around Jira’s problems by splitting the work into separate projects, but then they’re almost completely siloed, and Jira doesn’t help you connect them up. The other problem I have with it is that it’s too fussy about the hierarchy of issue types. You have sub-tasks, stories, epics, and initiatives. Each one has special semantics and certain supported operations. If you started defining some work at the wrong level of granularity, too bad, because switching everything to a different tier is complicated and massively slow (literally a multi-page wizard, a progress bar and a confirmation screen when making a “mass edit”, i.e. a trivial edit to two or more issues). Hierarchical issues is a good idea, because that’s a very natural way to break down and refine work estimates, but it should just be an arbitrary tree, not a strict and limited set of tiers. Too much complexity, not enough generality. (And not enough speed.)