You can use 2D Toolkit (2.3) with Unity 4.3, use as little or as much of each system as you like. Unity provides some really nice tools, but 2D Toolkit builds on that and does a lot more. Some examples - I'll update this later with more stuff, maybe set up a "comparison" website - I say that loosely, as I think you should probably use the strengths of both systems.
1. Atlasing in Unity Free.
2. Pixel perfect camera and camera adjustment for different resolutions.
3. Platform collections (atlas swapping for different resolutions)
4. Bitmap fonts, including bitmap fonts in atlases.
5. Tilemap with optimal collider / render mesh generation.
6. Sliced, tiled and clipped sprite using the same shader.
7. Sprite dicing. http://www.2dtoolkit.com/docs/latest/advanced/sprite_dicing.html
8. Super fast animation set-up workflow.
9. UI components.
10. PNG atlases - you can choose to trade of a little load speeds for significantly smaller builds.
11. Static sprite batcher.
12. Awesome community driven features - 2D Toolkit owners get an opportunity to shape the product.
2D Toolkit 2.3 uses a fair few Unity 4.3 features and interacts really well with Unity sprites.
1. Render layers and sorting order works together with Unity sprites.
2. 2D physics - you can swap between 2D and 3D physics pretty quickly. http://www.2dtoolkit.com/docs/latest/unity_43_integration.html
Unity 4.3 can do some things that tk2d can't do due to Unity scripting limitations.
1. Animating colors in the Unity animator
2. Automatic atlasing in Unity Pro
3. Animating scaling hierarchies of sprites using the Unity animator.
4. Possibly better batching performance for lots of single sprites. 2D Toolkit isn't exactly slow to start with.
5. Automatic collider & sprite shape detection. (This is not a scripting limitation, but we've not had enough requests for this)
You can mix and match both - use the strengths of each as you see fit