As far as I can tell, Jira sells well to enterprises because it focuses on features that enterprises like (lots of accountability and metrics and charts and graphs and shit, extremely configurable). But it doesn't sell well to developers on the ground because it's slow, its extreme configurability ends up screwing with developer productivity, and it's not a pleasant or easy interface to deal with.

I don't foresee the end of Jira any time soon, but I do think that they will go the way of other enterprise bloatware eventually.