Blame religion and politics on the lack of the seven kingdoms including the Riverlands. After some of the victories of Aegon the Conquerer the High Sept stated that is the seven gods divine will that Aegon conquer the seven kingdoms, there are seven kingdoms and seven gods but these gods are all facets of the same divinity. Aegon never conquered Dorne. Thus the Riverlands become a kingdom even though it wasn't originally.

Now the Riverlands before Aegon the conqueror were never a "kingdom" they were lots of castles and lords that were conquered via the Iron Isles. Harren Hoare also known as Harren the Black ruled over the Iron Isles during this time as well as the Riverlands and the terrority that will become Harrenhall. He didn't bend knee to the Dragon Conqueror and his impenetrable castle was vanquished with dragonfire. Aegon the Conquerer split the Riverlands and the Iron Island as two kingdoms the Greyjoys get the Iron Islands and the Tulleys, both being made into major houses for they weren't before.

Now the Highgarden and Baratheons weren't originally great houses. The Highgardens the stewards of House Gardner become a major house when Gardner died in dragonfire, and the stewards gladly bent knee. House Baratheon on the other hand was founded via one of Aegon generals (Orys Baratheon) a rumored half brother of Aegon who was a bastard (and thus part Targaryean via blood but not via name.) The general took the defeated Stormking lands as well as his daughter as his wife. Now king robert also has more Targaryean blood in him due to the fact his grandmother was also a Targaryean (and thus why he is king instead of Ned or Jon Arryn, Robert claim was better).

The 9th territory is the Crownlands such as the territory surrounding King's Landing and Dragonstone (Stannis island where Aegon first conquered and waited till his dragons were ready.) This territory was never hold via any kingdom for very long prior to the invasion and was always contested.

So via claiming the Riverlands and the Iron Isles as separate kingdoms Aegon could claim he fulfilled his divine destiny and unite the seven kingdoms as one kingdom united under one banner like the seven are one and the one are seven. Just ignore the failure to capture the Dorne like the Alexander failed to conquer India.

Now the Dorne eventually become the seventh kingdom and the Iron Isles and the Greyjoys demoted due to Dorne become part of the Targaryean kingdom via marriage. The kept the name 7 and drop the Greyjoys due to Politics and Religion.