Here is what I take to be the gist of your analysis:

• Gen1's narrative is organized around three rebellions against Grandbell.
• The third rebellion is carried out by the protagonist.
• Players expect the protagonist to triumph, so seeing Sigurd's rebellion end in tragedy is simultaneously subversive (protagonist fails in his mission) and consistent with the established rule-of-three. This structure helps make Gen1's narrative more effective.

I don't buy this analysis.

1. One definition of "rebellion": an effort by many people to change the government or leader of a country by the use of protest or violence. If we use this narrower definition of the term, Verdane's invasion and the first Grandbell/Augustria war would not qualify.

2. Another definition of "rebellion": an act of violent or open resistance to an established government or ruler. If we use this broader definition of the term, Sigurd's wars against Verdane, Augustria, and Grandbell would all qualify, but so would other battles, eg. the Orgahill pirates skirmish.

3. Setting aside issues of definition, Augustria rebels twice, under very different circumstances and with a full year separating the incidents. It is difficult to frame this lengthy ordeal as an uninterrupted "middle act."

4. Alvis rebels against Grandbell and succeeds. He manipulates a sickly king, he marches key armies away from the capitol, and he sends political opponents to their deaths. These actions fit both definitions of "rebellion."

5. The Lopto Clan rebels against Grandbell and succeeds. They usurp control of the capitol via Alvis, they carry out assassinations, they manipulate Alvis into fathering their deity's vessel. These actions fit both definitions of "rebellion."

There are more than three rebellions no matter how we define that term. A successful rebellion against Grandbell is the defining moment of Genealogy's story. Your thesis doesn't seem to hold up.