I think it would be a good idea to have the Object browser(shift-F4) somewhere in the File menu and allow the user to do things like rename and delete datablocks there. Maybe by double clicking an item, you can go directly to the window type that the data is used in so you can quickly modify it as well.

Being able to set a z-offset for procedural brush textures would be great so that you don't have to use the same brush sample when texture painting in Blender. Also, caching multiple samples with a z-offset and cycling through them each step would help to add some variation to your brush strokes.

I think this is just a minor inconsistency in the current interface. I think if we were to move the “Add” and “Timeline” menus to the 3d view and timeline windows respectively, it would better communicate their functionality to the user. The “Timeline” menu would also make sense in the buttons windows, since this is one of the windows open by default that allows you to change the current frame without using keyboard shortcuts.

For external resources, I often don't bother to click the "relative paths" button, so it would be nice to be able to set a path to relative without opening the fileselect or change the path manually. I don't think alt-click does anything when opening the file browser, so perhaps this could be used?