I suggest to add an alpha channel to the color value to control the transparency through the selected color and not by the layer or brush only. This feature give you full control over the transparency of the color you're painting with.
Right know, I you want to have a transparent color you always have to add a new layer and reduce the opacity. If you want to draw with 3 different transparency values, you need 3 more layers. Of course you can merge them, but then you can't influence the color anymore.
With this feature you only need one layer and you are able to change the color and opacity and and paint over again.
