When saving a PNG image, you have the option to save colors from transparent pixels. This is not possible to use because almost every operation in GIMP (resize, merge layers...) is replacing transparent pixels with a black color. 

This is bad because fully transparent pixels are clearly visible when using bilinear interpolation in a game.

This is bad when the alpha channel is used for something else than transparency. I mostly use the alpha channel for bump mapping.

When for example, applying blur to an image, it should be possible to either treat the alpha as transparency to avoid color artifacts on edges or treat alpha as just another color channel where blur is applied. This property should be an explicit option when adding an alpha channel to a layer.