I started to learn how to create 2D games with the Unity3D engine. I found two plugins: NGUI and 2D Toolkit.
My problem is that these plugins have duplicate functionality, both work with sprites, animation, etc. I can't work out which is better to use to create 2D game.
You will have to do some research to answer your question. One of the main problems in making 2D games with Unity (using sprites) are performances issues.
It is common have performance problems with free alternatives like the free version of Orthello or the 1st version of Sprite Manager. I never used 2D toolkit, but I believe that unity community has a lot of users who has purchased a 2D toolkit license and you can find help in their foruns and comparisons with other 2D tools like ex2D and etc.
I recommend you to read these (good) tutorials
http://www.rocket5studios.com/tutorials/make-a-2d-game-in-unity3d-using-only-free-tools-part-1/
The second one was posted in the unity official blog and I believe that you can solve some of your doubts there.