Rive is closest sonce they have scripring support.

Threejs is a 3D graphic libary, something different. And godot web I never used but know of as a game engine, not a scriptable animation tool.

As Godot is still very simple from the UX perspective, I'd prefer a set of tools to fully replicate the flash workflow instead of a dedicated app. Why reinvent the wheel? Stuff like keyframe animation editor etc is already there anyway and the engine is powerful enough. Just missing some tools, which could be easily added via the asset store.