It's so funny that this is the way it's become, as Atlassian grew up being the cheaper, simpler alternative to extremely expensive, super opaque, ultra closed source systems like Clear Case. I remember a time when Atlassian actually raised the prices of Jira's top level of support and service because enterprise CTOs were confused by such a low price point.
Ten years ago I made exactly this migration for a SaaS shop's helpdesk & dev team. At the time JIRA was easily the best value & most customisable solution for integrated ticket tracking. I learned Java & Groovy to write extensions for it. It wasn't just CTO/CIO friendly, JIRA really was the great choice at the time in both UX and ease of implementation. Especially if you'd been bogged down hacking RT or GNATS or permanently scarred by anything from Rational.
What I realised is that eventually they're all ad-hoc, informally-specified, bug-ridden, slow implementation of a workflow engine and metadata service. Your choice is mainly of the interface and domain-specific layering violations.
Troll-friendly soundbite: Atlassian is the new Rational.
