Welcome to the forums @Cirneco!
I personally would not worry too much about the structure in the beginning of any project, even a serious one. The thing is, you will likely not know what structure you need, how reusable the code will be, or even if the project concept is viable until after the first initial prototype. At that point, once you have a initial prototype, you will have a much better idea of what the project needs going forward, and how you might structure your project around the needs discovered during its creation.
So, for this reason, I would at first focus on getting a solid first prototype. That is not to say throw caution to the wind and make a messy structure or something, but instead, just choose what you think is the best for you and make the prototype using that. Spending too much time structuring and planning could lead the project to sitting for long enough that the enthusiasm around the idea dies, you no longer have time for it, and/or a new idea pops up and the process starts all over again.
Though, to answer the question in the topic: No, I would NOT make everything a plugin as a design standard. Games generally need to have tools tailored specifically to them, making the reusability of the plugin kinda limited. Additionally, you will be sinking time into making the plugins rather than making the game. If you think a plugin would help and be reusable, then go for it! But I would not go at the project trying to compartmentalize code into plugins as a design choice.
(Granted, this is all based on my personal experience, so please take everything written with a grain of salt!)
