There's a lot of truth to that, but Jira (or more accurately Atlassian) does things that are worthy of hate too.

- Some information is displayed in unexpected places

- The application can be slow to load

- Customizations are confusing (Do i need to edit the screen, the screen scheme, or the issue type screen scheme?)

- Confusing options (Field configurations have both a "Configure" action and an "Edit" action.)

- Basic features are often left out and require plugins to bridge the gap.

And much more!