yeah, I really didn't want to use video. The vectors are around 64kb per cut scene. I don't want to create several Mb worth of mp4s for each one.
Did you give it a try? If the scenes are quite short, I found webm to have a reasonable small size.
But .. it bothers me of course as well, having a full video of rastergraphic what could be just some vector and animation data.
I haven't tried with webm. But they need to play full screen on desktop and also stream well on mobile.
I might try Spine, I've heard some positive things. They'll still end up as textures in pixi but maybe at least they can pack well.
Pixi is great for anything that is a texture, then it is really fast. Otherwise it is not a flash replacement.
I do not use it for vector animations, but spritesheets or a webm video overlay is what I would use in your case.