There actually is conceptual reasoning behind both styles. Wikipedia on the relational model and graph databases gives good overviews of this.
The primary difference is that in a graph database, the relationships are stored at the individual record level, while in a relational database, the structure is defined at a higher level (the table definitions).
This has important ramifications:
- A relational database is much faster when operating on huge numbers
of records. In a graph database, each record has to be examined
individually during a query in order to determine the structure of
the data, while this is known ahead of time in a relational database.
- Relational databases use less storage space, because they don’t have
to store all of those relationships.
Storing all of the relationships at the individual-record level only makes sense if there is going to be a lot of variation in the relationships; otherwise you are just duplicating the same things over and over. This means that graph databases are well-suited to irregular, complex structures. But in the real world, most databases require regular, relatively simple structures. This is why relational databases predominate.