General PM software gripes (jira, project, pivotal tracker):
1. lack of keyboard shortcuts: have to use mouse way too much. org-mode is so much more intuitive and efficient for task management once learned but lacks collaborations and no one wants to put in the time to learn it.
2. Difficult to get a clear picture of the overall status of projects. Project managers have to spend a lot of time gathering status updates and creating reports because we use so many different tools, and the built-in reporting generally sucks.
3. Lack of intuitive structure within data. An ideal PM platform would structure information in an intuitive way that to make it discoverable by people working on peripherally related projects.
Specific gripes w/Basecamp:
1. Don't get notifications when clients upload files, only when they post messages (they often don't understand the difference)
2. Checkboxes to send out email notifications are not checked by default for new messages. Clients always forget to do this, even when we remind them, and then wonder why we don't respond right away.
3. Refusal to use gantt charts. I get that 37signals has a philosophical objection to dependancies and detailed timelines in PM, but sometimes a gantt chart is the best way to visually display a project timeline, especially if certain milestones are missed and impact the rest of the project.
I think Remember the Milk has a decent solution for search, but obviously it's not nearly as complete as Basecamp.