One task where GeoJSON falls down is simplification of a group of polygons with common boundaries, e.g. the 48 conterminous US states. If you start with a highly detailed set of polygons, you need to simplify them for practical display in an online map. GeoJSON doesn't encode the fact that the boundary points are common between adjacent polygons. When you simplify those polygons, each one is handled separately, and y…
From what I can tell, the top criticism of GeoJSON is the under-enforced winding order specification, and crossing the antemeridian.