After discussing with the Devs, the reason we don't currently have animated GIFs support in Roll20 is how the tabletop is rendered. When the screen refreshes, it displays what is essentially one giant image. It first processes all the visible graphic elements and how they're layered atop one another. Then it creates a single flat image from this and displays it on your screen. Presently if you upload an animated GIF file, you'll only ever see the first frame of the animation. Back when we had the old render engine, there were bizarre events that would happen when you transformed an animated GIF in Roll20 - the transformation manipulations only affect the first frame but not for the rest of them for example.
For the above reasons, we're not planning on implementing animated GIF support at this time.