I hate to make a suggestion as I know Scirra's plate is so full... But there is something I see as a major necessity as a game gets larger.
The Z-ordering at the moment gets very irritating, as it is very difficult to specify what is on top of what if there is a large number of objects, especially if they are not to be in the layout at start.
A good solution would be to be able to specify the z-index of objects at edit-time (and runtime, why not ;) )
An excellent solution would be a vertical list of all objects that could be accessed, and the objects moved up and down the list to specify what is on top of what.
That would be a fantastic and welcome solution.