I am making a game in which the server has full control of the entire game.
This allows people to make their own multiplayer games very easily.
This game will also support Android.

Question, should this game be 2D or 3D?
Or should I make just 3D because people can fake 2D games using GUIs and other stuff?

How long is a piece of string? There's no way to answer the question without knowing more about the game itself. That said:

• Faking 2D with 3D is a trap, because you get all the difficulties of working with 3D with none of the benefits.
• Android supports 3D by definition -- its very specification requires hardware with OpenGL support. On other platforms it's not as guaranteed as people think.

Hopefully this will help make a decision. Cheers.