Chrono Sword's developer David SpaceDuck created a sprite tool called Lollo that turns 3D animations into pixel animations.
As the developer explains, it is a kind of a skeletal animation system. You build up a character using multiple sprite parts and then apply animation data so it starts moving. However, normally it works with 2D art, and Lollo can make pixel animations from 3D artworks.
Compared to other animation tools, Lollo can firstly animate in every direction. With 2D animation, you spend a lot of time drawing and animating characters in every possible direction. When you use 3D positioning, you can easily create movement in any direction you want.
Secondly, Lollo separates animations from the character. This allows you to blend motions which creates smooth transitioning between the character's actions. Plus, it means you can reuse animations for different characters.