[perrygeo]

Partly true, but don't blame GeoJSON. Blame the data model.

GeoJSON is firmly rooted in the "simple features" model of spatial data. Sometimes called the "vector data model", this is ubiquitous in GIS. Each geographic entity (aka "Feature") has a single geometry and many non-geometry attributes. Each feature is independent.

The vector data model (for better or worse) is the basis of many systems because it fits the tabular/relational style so closely. What is a feature but a row in a table plus a special column describing its geometry? Topological relationships are ignored by design.

TopoJSON, ESRI coverages, the internal OpenStreetMap data model, and a few others are notable exceptions. They explicitly handle spatial relationships, at the cost of making the model unintelligible to row-based processing.