When comparing Puppet2D vs GAF:Flash to Unity, the Slant community recommends Puppet2D for most people. In the question“What are the best 2D animation tools for Unity?” Puppet2D is ranked 7th while GAF:Flash to Unity is ranked 9th. The most important reason people chose Puppet2D is:
Instead of having to change sprites to bend legs or other joints mesh deformation changes the mesh shape based on joint weights to bend and move.
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Pros
Pro Mesh Deformation
Instead of having to change sprites to bend legs or other joints mesh deformation changes the mesh shape based on joint weights to bend and move.

Pro Inverse Kinematic bones
Bones will move and rotate reacting to the position of the rest of the skeleton. The animator does not have to animate each part of a joint but rather have it follow realistically. Also can be used for ragdoll effects based on physics.
Pro Built on top of Unity’s animation system
Mecanim and state machines work natively since Puppet2D builds on top of Unity’s built in animation system.
Pro Can convert 99% of what can be done in Flash
GAF supports such Flash features as:
Masks support;
Filters support;
No limitations on timeline;
Conversion of shape tweens;
Frame labels.
Pro No need to use large Sprite Sheets
With GAF converter you get a highly optimized texture atlas and a config file. You don't need to take trouble over cumbersome sprite sheets. You can easily modify an already working in Unity animation and play around with the animations parts whenever you need.
Pro Alows using Flash animations in Unity
You can convert Flash animations directly in Unity with the help of plug-in. The converted .gaf file consists of a texturte atlas and a binary config.
Pro Supports different frameworks
Full playback API supported in Unity3d, Cocos2d-x, Cocos2d, Starling.
Pro Light, fast, and optimised
GAF is lightweight and fast in a project.
Pro Uses dynamic text
GAF can use dynamic text in animation on some platforms.
Pro Can customize sprite animation
GAF can swap a sprite with another.
Cons

Con Forced editor scaling causes problems
Puppet2D adjust the scaling of bones in the editor for display purposes, which results in unintended behavior if other objects use a bone as a parent.
Con Sound support available only in Premium version
GAF Converter supports sound but only in the Premium version.

Con Doesn't support sounds
GAF does not support importing audio along with Flash animations.
