Discourage custom `System::setup`

This issue is split out of #437.

Using `System::setup` for initialization, while often being convenient, brings three major drawbacks with it:

* implicit resource creation -> might be using the wrong resource, especially when generics are involved (one system uses `Foo`, the other one `Foo` and both will fail to see the changes of the other one)
* initializing system fields with it means:
* fields need to be `Option`s
* resource initialization is decentralized (whether one considers that as a drawback or not)
* resources / system fields can hardly depend on each other when initialized using `setup`, possibly leading to (undocumented) ordering requirements of the setup calls