1. It's extremely slow.
2. It's difficult to predict the effect of making any kind of change.
3. The permissions system is so convoluted, I can be the admin of a board, and yet not have permission to see a ticket on it.
4. It relegates the conversation to a second-class UI element, when this is the most important part of any project management system.
5. Trying to operate on a bunch of tickets all at the same time (e.g. move all tickets in this status into some other status) requires a lot of time.
6. Every Jira setup is so different, trying to compare a piece of work from one area of the organisation to a similar piece of work elsewhere is useless.
7. The UI is extremely buggy. I can add a mandatory field to a ticket, then when I try to use a shortcut to create a new ticket, it won't work because I can't fill out that mandatory field.
8. There are random side-effects when one person does something on one bit of the system, and VOILA everybody's workflow is broken, with no obvious warning that would happen.