Godot provides base nodes for making menus, then you have to code a bit to execute the actions you want. In the next version 2.2 however you'll be able to use visual scripting like Unreal blueprint: http://www.gamefromscratch.com/post/2016/08/07/Godot-Engine-Visual-Scripting-First-Look.aspx (people can try it already if you compile the engine yourself from Github).
I don't think there is a plugin for doing MMO yet. In fact this is so complex I don't think it would just be one plugin, and certainly not easy to deploy. Anyways you have to code it too.
You can remove or change the splash screen in scene -> project settings -> application -> boot splash option. There is no watermark, only a splash screen.
You can import 3D models from any 3D software, you have to export them in OBJ or Collada first: http://docs.godotengine.org/en/latest/tutorials/3d/importing_3d_meshes.html#doc-importing-3d-meshes.
FBX is not supported for licensing reasons: http://docs.godotengine.org/en/latest/reference/faq.html?#why-is-fbx-not-supported-for-import
I never animated a 3D model in Godot so I cannot answer your last question. But I believe it's possible, for example the 3D demo project included in the demos package shows you can have 3D animations.
Sorry for being short at answering but you are asking too many things in one post. This is a Q/A website, there should be one question per post. Also, read the documentation and do some search before asking, you will find a lot already.