Thanks for the feedback!
The transition animations are done with a CanvasLayer node that I add to each scene. The CanvasLayer has an AnimatedSprite that contains all the frames of the animation--I rendered out the animation in Blender to the size of the screen. Then, when a Node somewhere wants to change scenes, it tells that CanvasLayer to do the fade-out animation, and then the CanvasLayer will change the scene. That CanvasLayer will also play the animation when it is added to the scene, which creates the fade-in.
I actually first used a technique like this in this game--the only thing interesting about it there is that it is not locked to the screen size. To do that I rendered an animation of a single square fading in and out so that it could be tiled horizontally and vertically.
I'm glad you liked the character animation! Also I'm glad there wasn't much lag.