Neo4j

That pdf is from presentation that was used for a thesis defense and does not represent an implementation pattern. You'd want to use apoc virtual nodes

AFAIK it's a quirk of the Neo4j browser on what it displays in different output modes. Not everything in the result set is included when the results are viewed in text mode. All the data is there and you will see the full result set in table mode. ...

You might want to try this R project / CRAN package to connect to Neo4j from R. It uses the Neo4j cypher-shell command line tool to send queries and retrieve data from the graph which makes it fairly lightweight implementation.

Use cypher-shell if you want to see the relationship types in the output.

Yup... try new pattern. Cypher queries do not have to be just (node)-[rel]->(node). They can, and should be as expressive as possible in most cases.