When comparing Puppet2D vs 2D Toolkit, the Slant community recommends 2D Toolkit for most people. In the question“What are the best 2D animation tools for Unity?” 2D Toolkit is ranked 3rd while Puppet2D is ranked 7th. The most important reason people chose 2D Toolkit is:
The documentation for the toolkit is well written and there are video tutorials as well as an active community.
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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 Good documentation
The documentation for the toolkit is well written and there are video tutorials as well as an active community.
Pro Includes source code
No need to pay more to get access to the source code.
Pro Pixel-perfect camera
Pixel games in the style of 8 or 16 bit systems need to have each pixel uniform on the screen which 2D Toolkit supports with a camera component.
Pro Add colliders in the atlas editor
Choose from either a box, sphere, or mesh collider that will output as either a 3D or 2D collider in Unity.
Pro Create different resolutions of atlas
2D Toolkit allows for different sizes of atlas from 1x, 2x, or 4x which can be changed depending on platform resolution.

Pro Built to work inside Unity
2D Toolkit is an editor extension so users don’t have to leave the Unity engine for tile mapping.

Pro Create Atlases within the tool
Create sprite sheets for tiles to save draw calls and to keep tilesets organized.

Pro Supports the Tiled TMX Format
Create tilemaps in Tiled and implement with 2D Toolkit.
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 Doesn't integrate with Unity's Sprite system
2D Toolkit provides a completely proprietary sprite implementation. Though it can be used alongside Unity's 2D systems, the two are completely separate and require different code to utilize.
