Been writing Lightning components in IC for a while now and one thing I have found which can get a little messy is working with the different parts of a Lightning bundle.
I'm not sure if this is within the boundaries of what you can develop for the IDE, but I was thinking perhaps it would be nice to allow the file tabs at the top to display a dropdown when clicked which allowed you to select which file within the bundle you want to open. This would reduce the mess in the tab set.
If you wanted, you could perhaps drag the files from the list into the tab set if you needed to (ideal for instances where you may want to split the view which I do on regular basis).
Just an idea anyway. Nothing important. :)