Unity added 2D support with their 4.3 release of the engine. The 2D package comes with options for both sprite sheet animations and bone based animations with the added support of Mecanim, Unity’s new animation solution.
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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 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 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 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.
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.