For a smaller project, though, I would roll your own to specific requirements, or would use a smaller package or product - because JIRA does everything and that could be too much sometimes.
From an end user point of view, JIRA is bad because it is slow, has a bad user interface, and really doesn't quite fit most workflows. If you're trying to track a trouble ticket, which is what JIRA was originally designed for, then it will perform the job adequately. However, anything else forces you to fight more against the system design to get things just the way your work process needs to be.
I'll take these one at a time:
1) "These have all been tacked in and the fact that they are all an afterthought really shows through in how you setup and manage JIRA projects."
Slowly, but surely, Jira is going to a consistent role/schema/custom field mechanism format for managing issues. Jira _did_ start off as a "Software Defect Tracker", and, if you look closely, you can still see the DNA in the product, but, with things like issue-type-screen schemes, and custom workflows - you really can make it look like whatever you want.
2) "Jira is slow" -
I don't know how one makes it slow. I suppose it's possible. But our 8 Gigabyte Hard Disk, 2 Gigabyte Memory virtual machine currently has 45,000 issues that it's tracking, and searches come back pretty much instantly. Perhaps your Issue database is a lot larger than ours. I find it hard to believe your virtual machine is slower.
3) "Bad User Interface"
- simple. Straight forward. Create, Edit, View, close. Dashboard for custom views of your data.
4) "Doesn't quite fit most workflows"
- Uhm, it has a world class workflow _editor_.
5) "Trying to track a trouble Ticket, which is what Jira was originally designed for" -
Now we're going to inaccurate to completely polar opposite of reality - Jira was originally meant to go head-head with Bugzilla - Jira is a take off of GoJira, which is an alias for Godzilla, from which Bugzilla is named courtesy of Mozilla. Yes, it is rather indirect. Anyways, the point is Jira _evolved_ into an issue tracker from a defect tracker, in much the same way quicken evolved into an accounting package from a personal finance tool.
Anyways, as One who just spent four years using (and dearly loving) jira, and is now having to suffer the absolutely and utter agony of "Upgrading" to a Remedy ITIL suite, I can tell you that the Jira interface is a delight compared to this godawful web interface in Remedy. Now _that_ is a bad user interface - I challenge any remedy user out there to argue differently.