Aseprite
As a summary, it's like Easytoon but with colors and layers.
You can define frame duration in ms, look at onion skinning, have opacity layers, or other methods to add layers in different ways (difference, lighting, ...)
And there's gif export, of course, however, I'm unsure if it can manage hundreds of frames in one single project.
Basics of what we can do with this :
https://www.aseprite.org/docs/
And for those who already knew about the existence of this software and saw that it costs money, I'll quote the FAQ :
You can still download its source code, compile it, and use it for your personal purposes.
https://github.com/aseprite/aseprite
So what do you think ?