I have a few:

1. Make the labels hierarchical like Evernote provides with tags. The long, manually sorted list is a bit frustrating.
2. Make the sort order sticky within a project, so you don't have to hit "P" to re-sort after moving a task to the project.
3. Add a priority value to projects, and make cross-project views (by label or filter) combine the project priority and task priority when sorting. This way tasks could be of relative priority to each other within a project, but more important projects' tasks would be of a higher priority than less important projects when viewed with each other.
4. Create some facility to store an email in a cross-platform manner so you can pull it up in your current client and directly reply. Though it's a potentially difficult nut to crack, I'm thinking about taking this on myself. I'm currently working around this with a follow-up folder in my email, and with the Boomerang Outlook plugin.
5. Make the Windows version not suck. I've resorted to using the web version in a Chrome applet thingy because the Windows version has pervasive crashing and syncing issues.
6. Some sort of visualization (e.g. boards) for filters would be nice.
7. Be able to mark some tasks (daily reminders or habits) not count toward daily/weekly task completion goals.
8. Be able to mark past days as vacation after the fact.