One other idea I think might be nice would be to use the empty space below the shortcut tray to allow users to save shortcuts to custom views that are not included in the standard shortcut tray. This could either be a second tray or just an extension of the standard one.
I don't particularly care for the new color palette but it sounds like you have a long-term strategy for themes and I think that is a good solution to address everyone's preferences.
Two things from a UI standpoint that bother me though...
1) On the iPad, I don't like that the task details pane stays populated with the last task I viewed even after tapping on another view via the shortcut tray. At that point, my focus is no longer on that previous task I was viewing and I find it distracting to have it still visible on-screen (especially if it doesn't actually exist in the view I have switched to via the shortcut tray.)
2) On the iPad, if I am in landscape mode and tap to edit a task title (via the task details pane) the UI rotates to portrait even though I was using the app in landscape.
I do have to say that even with these issues, I am MUCH happier with the direction the app is going compared to the previous iPad version.