I've used Pivotal Tracker and I think it's great for small teams, but I can not see a big company with 500+ users using it. JIRA is better for ticket tracking, issue linking, cloning, reporting, integration with Bitbucket/Github branches, user permissions, build system integrations, burndown charts, analytics, media services support, and not to mention the ecosystem around JIRA is just huge.

Disclosure: I'm an Atlassian employee, but I had these opinions before I started.