Its real problems are a polarizing UI (I like it, others hate it) and flexibility that leans toward bloatware-level complexity. But you can configure it to look/feel as simple as Trello, of course.

To beat Jira for me, you'd have to do something revolutionary, like having the entire issue tracker hosted/versioned in git (so issues are inherently tied to code in some way).

I haven't thought that concept all the way through, but it seems like the only way Jira fails me -- when I need to manually tie issues to commits (even though it can be as easy as using a hashtag).