Personally, I love JIRA Agile. However, we also have some projects within our organization that use Pivotal Tracker, and many employees prefer Pivotal Tracker to JIRA Agile. Here are some things that I have heard Pivotal Tracker does better than JIRA Agile, that I think might get more people (at least within our organization) to use JIRA Agile:

• Separation of backlog vs. icebox. Having everything in the backlog makes it difficult to maintain. Having a concept of an Icebox (features that you don't know are a "go" yet) is a major plus. You can configure JIRA Agile to use filters to separate out backlog vs. icebox (perhaps using labels), but it is more difficult than it should be. Backlog and icebox tickets should be a built-in concept, rather than something you have to configure to get working right, and then train users to use correctly.
• Velocity calculation: It is not obvious what the velocity for the project is, and the way that velocity is calculated is not very configurable. The velocity for the project should be right in front of everyone on both the planning and current sprint boards. It wouldn't hurt to have a way for you to see more details on the calculation of the velocity, either.
• Future sprint planning. Pivotal Tracker automatically organizes all tickets in the backlog into sprints for you. You can easily drag-and-drop issues in and out of sprints, but PT doesn't force you to manually create each sprint, it just automatically calculates the next several sprints based on the velocity projected for the project. This is a BIG deal in my mind (being a JIRA agile fan) as well.
• Team member strength in velocity calculation is also a big deal. For us, the teams change regularly, and having a way of indicating that we are not at 100% capacity in team strength, and having that affect the velocity projection is really useful.
• Because JIRA supports customizable fields, I think it would be imortant to have a more advanced configuration screen for the boards to allow the admin of a JIRA project to configure the fields that are shown in the issue lines and the issue details screens. Also, all fields that are on the issue details screen should be editable within JIRA Agile. Having to swap from the JIRA Agile screen to the native JIRA edit screen is not intuitive.

That's all I am aware of for now. I hope these suggestions help make JIRA Agile even better. I would love to continue using it.. But, being one of the only ones, I'm fearful I may not be able to forever unless some of these suggestions are addressed.