I think it would be very useful if, when you changed layers, it showed what was in that layer. This could happen very briefly, or have a light dashed/moving outline around sprites. There have been tons of times where I couldn’t figure out what layer something was on, or started doing something on the wrong layer.
Please correct me if something like this already exists.
You can change the opacity of non-active layers here:
You can also select Flash layers when it is selected which will make the contents blink white momentarily when you switch to a layer, but it only seems to work if you cycle layers via keyboard commands, not clicking.
Another trick that helps a lot is to simply ctrl+click on something with the pen selected. Holding Ctrl changes to the Move Tool and holding Ctrl with ther Move Tool enables the Auto-pick layer option. What this does is it will select the layer of the pixel you clicked on. It’s the feature I use the most in this program by far.