I think the folder idea is great. I, too, never understood the need for sub-animations and had a few game prototypes where the list of animations became... a little unmanageable. So folders would be fantastic.
Another suggestion to the new animation system would be to better integrate it with the picture editor. It would be a lot more productive if you could add, delete, move frames, set speed, loop and preview straight from the picture editor. In my opinion, the Animator tab could be completely removed, then the Project tab would be used instead if you need to organize animations folders.
I like this a lot. One less tab would save a lot of clicks and increase workflow. In addition, it was always cumbersome to have to move in and out of the image editor to change animation settings. A preview button would be fantastic to verify the smoothness of the animation without have to preview the game every time.