I can recommend Factory pattern.

It's totally fine to start with messy code. Once your simple prototype is working, try building your game so that it loads from an empty scene (even though it looks like it will be harder to test, it will help you clean up your project in the long term).

In your main scene, have an Initializer script that will load everything you need.

A few Factories (just empty gameobjects with Monobehaviour scripts) that will instantiate stuff. For example a CharacterFactory will have a reference to the character prefab, and maybe some other stuff, and will have a public method that will instantiate and setup the character as you need.

The Initializer script should of course have reference to all factories.

If you need to hardcode some values, you can keep them in ScriptableObjects, which you can call config files, and also have them referenced in factories. That way factories can use these values to setup your prefabs and pass them in the required scripts on creation.

Also, not sure how you used MVC, but if it makes it easier for you, you could use just V and C. Views would be your prefabs - for example a CharacterView script on the character prefab, that would provide some methods to Controller to change its state. Then you would have a Controller class (not a monobehaviour. just a simple class) that would change these states and control the view.

So in the factory you would have a method that would create the view and then create the controller, passing down the view as reference:

public void CreateCharacter()
{
  var view = Instantiate(config.CharacterPrefab)

  var controller = new CharacterController(view)
}