You should ditch current transition system in favor of something called "wipe files".
You have grayscale image which size is same as game screen size like this:
And now...
- When user select fade in with wipe file, first lightest pixels (closest to white) from image are removed revealing next scene underneath
- When fading out it is reversed.
This would be more customizable IMO as user would be able to make own transitions.
Yeah, I know it is possible via code mode, but this is closer to idea of Stencyl - making game without single line of code.