When comparing Unity 2D vs Marionette Studio, the Slant community recommends Unity 2D for most people. In the question“What are the best 2D skeletal animation tools?” Unity 2D is ranked 5th while Marionette Studio is ranked 11th. The most important reason people chose Unity 2D is:
2D game creation was a major feature request from the Unity community and was added with version 4.3. 2D is provided in both the Pro and Free distribution of Unity.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Built into Unity 4.3+
2D game creation was a major feature request from the Unity community and was added with version 4.3. 2D is provided in both the Pro and Free distribution of Unity.
Pro Integrates with Mecanim
Mecanim brings state machines and blending to 2D bone animation. The state machine editor allows for designers and programmers to visually create a Finite State Machine (FSM) to control when animations should play. Mecanim also allows for blending so an animation can transition smoothly between two states without the need of in between frames made by an animator.
Pro Sprite Sheet and Bone based animation supported
Both types of 2D animation for game development are supported in Unity’s system and can be used interchangeably in the timeline.
Pro Easily change sprites dynamically
Usually used for character customization, programmers can change any sprite in a bone animation at runtime easily by referencing the bone and loading the new sprite from the resources folder.
Pro Actively maintained
Marionette Studio team is actively involved in the development of this software. There is a changelog available and a public Trello board.
Pro Cloud based solution
Projects and files can be stored in cloud and the is no need for creating backups.
Pro Animation export
Animations can be exported as image packs and using some 3rd party tools can be imported and used in Unity.
Pro Easy to use
Can be used by anyone - intuitive interface and short learning curve.
Pro Web-based software
Easy to be accessed as no software needs to be download or installed on your computer.
Cons
Con Lacks critical features
- Vertices can't be animated, so you can't have ANY organic feel (like... lungs breathing).
- Parent bone can't be animated without affecting the children. This is especially impeding for organic feel, again.
- No option to show & unshow assets (or it is hidden), like for switching weapon on your character for exemple.

Con Poor script interface for texture atlases
Accessing individual sprites within an atlas texture is possible at runtime, but requires use of the Resources folder subsystem.
Con It's not free
Con No integration for major game development engines
There is no integration with major game engines such as Unity, Construct 2D, Unreal, Cocos 2dx, etc.
