Instead, I use a simpler approach. All my component systems know the required dependencies and explicitly synchronize components once per frame.
That's what I do too, and I think it's a reasonable approach. It's fine for that dependency to be encapsulated in the systems.
I have edited the diagram, now I have a render manager, and a render system component. It's better I think, what I don't know is, if the waypoint system should be a system or manager. It' has notihing to do with the entity itself... Hmm....
When you say "it has nothing to do with the entity itself", it makes me wonder if you fully understand the point of an entity-component-system framework.
In my view, all game objects should be entities. Not all entities have to have the same set of components - in fact most entities will just use a few. The waypoint has nothing to do with the player entity, say. But it is its own entity. I would think you would have a waypoint entity that is comprised of a Position and Waypoint component (and a Render component?). Or possibly the Waypoint component could describe a full series of waypoints itself (that would make it less trivial for them to be rendered, but then you wouldn't need some other component/entity that is responsible for connecting waypoints together in a path.
In your diagram, I would also question the lack of an InputSystem. Surely entities will need some sort of Component that describes how they are controlled - e.g. what input they respond to. So just like you have a RenderComponent and RenderSystem, you might want an InputComponent and InputSystem in addition to your InputManager which performs more low level/platform-specific tasks.
Also, you have a box called "Logic" above your engine. What do you envision going in there? I think the bulk of game logic should be in the systems or in individual scripts attached to the entities.