Jira is insanely configurable - if using jira is painful, that means that your jira admin has not configured it well for your workflow.
The config my company is using makes it somewhat more pleasant than stock bugzilla or trac (though not nearly as convenient as github issues was).
The amount of crap you can turn on if you like can make the interface completely unusable, of course. But that's true in anything with a lot of configurability. It's the cost of being able to build your own process onto the tool.
Small teams generally not looking to pay someone to spend a long time configuring their tools. Configurability is good, but I'd rather have sensible defaults if I can only have one.
The config my company is using makes it somewhat more pleasant than stock bugzilla or trac (though not nearly as convenient as github issues was).
The amount of crap you can turn on if you like can make the interface completely unusable, of course. But that's true in anything with a lot of configurability. It's the cost of being able to build your own process onto the tool.