Basic REST and JSON RPC are very simple to start with, but have common problems when application gets bigger. How do you represent relations, pagination, filter

Basic REST and JSON RPC are very simple to start with, but have common problems when application gets bigger. How do you represent relations, pagination, filtering etc? My go-to specification for structuring JSON documents is https://jsonapi.org/ https://jsonapi.org/ It covers most basic needs of a standard API.