Subsystem are designed to encapsulate logic and make them reusable and independent without having to extend Engine classes that share the lifetime with. If I create a plugin and sell it on the Marketplace, I would need the users to implement my Actors whereas if I package it in a subsystem then Users can still use their own.
This is true for having multiple subsystems, then, if I don’t have them the logic of that Actors will increase and users would be force to choose which base class implementation would need. Which is currently hapening at the moment. Basically, most Plugins that you can buy force you to use their Engine base classes (GameMode, PlayerController, Pawn… etc).