While I have learned and taught MVC and similar approaches, I find that when designing game architectures one usually has to be a bit more flexible. In unity I generally take the following approach.
I will create a few GameObjects to hold the necessary global logic. This would be things like the overarching state machine, networking, and sometimes control input. If anything needs to persist between scenes it will go here. Each object typically has one component script for game logic and one for temp/debugging functions that gets turned off or removed when not needed.
If the project has fixed levels I will make each level a scene and I will store level layout and other level specific information in the scene. If I am doing a more procedural project I will create a "LevelGenerator" object with component scripts that build and populate the level at runtime.
If I am building a system that has lots of mostly independent agents (e.g. enemy creatures) I try to keep the game logic and necessary state information for each agent as close to it in the hierarchy as possible. For example, the agent's position and rotation would be stored in it's transform. I might store the agents health, ammunition, speed, and current status effects along with the functions for moving, shooting, healing, and death in a component script on the agent's GameObject.
While there are countless other approaches that could work, I like this approach for a few reasons:
- It saves me from having to manually manage tons of data access in a central script. If I need to know where all the monsters are, I can just keep a list of game objects rather than using custom data types.
- When the agent gets destroyed all the local data goes with it. (No complex functions to clean up dead agents.)
- From a game logic perspective (on the projects I typically work on) it usually makes sense that each agent would "know" about itself and not about everyone else.
- I can still use all the OO goodies like polymorphism etc. when necessary.
This response likely says more about how I approach game design and software architecture than general best practices but it might be useful.
One note on encapsulation in Unity. Every component script you add to a game object has a bit of overhead. If your scene has a couple of dozen agents in it, than this is not a big deal and I would recommend trying to keep things as OO and modular as possible. If you are building a system with hundreds or thousands of active agents, cutting the components per agent from two to one can mean quite a bit of saved frame time.