The only thing I see in Jira as an actual gap is the inexplicable lack of a standard view for showing all of the tickets in a particular sprint. You can make custom queries, of course, but it’s such a common need which everyone else on the market solved in 1.0.
But the tool felt fairly fast and did it's core job pretty well.
The problem with Jira is the total disregard for UX. Very simple tasks like moving tickets out of a story take way too many steps when it should take one click.
They don't seem to want to improve it because of legacy customer or reasons....