When comparing Stencyl vs Unity 2D, the Slant community recommends Unity 2D for most people. In the question“What are the best 2D game engines?” Unity 2D is ranked 7th while Stencyl 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 Haxe scripting available for advanced users
Power users can also write code in Haxe (similar to Actionscript 3) to create their own custom classes and extend the engine.

Pro No coding required, great drag & drop interface
Visual scripting in Stencyl is based on the MIT Scratch project, which was designed to teach programming. Script elements fit together like puzzle pieces, ensuring that data and function types cannot be mismatched.
Pro Cross-Platform
Publish iOS, Android, Flash, Windows and Mac games without code.
Pro It's a NO-CODE Program, you can add logic without code
Pro The original concept for Ghost Song was created using Stencyl
The original concept for Ghost Song was created using Stencyl 3.x
Pro Great performance on every platform
Stencyl exports your games to native code so they have great performance on every platform.
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.
Cons
Con Not a powerful engine
Should be used for basic games only.

Con Only available via subscription
There should be an option to buy it outright, especially considering it is written by a one man team....this is not exactly an Adobe level enterprise with shareholders, so there is no excuse!
Con Slow release cycle
Con Updated
It needs much to improve for mobile games, it was left in the era of Flash games. In Android you can not even put the native keyboard, you can not access things like native camera, GPS or native text input.
Con Tile system is somewhat inflexible
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.
