>>56948009>Would Ruby and Sapphire be the way they are?Thanks for raising an interesting question.
RSE is reliant on the big kaiju fight between Groudon and Kyogre but if they don't exist, I think it can still remain mostly the same.
Magma/Aqua would still try to upset the balance of land/sea using technological means and you'll put a stop to their not-as-apocalyptic plans without any legendaries involved. Rayquaza would still be in the Sky Pillar in the postgame to represent natural balance and serve the Mewtwo role as usual.
For Diamond and Pearl without Dialga and Palkia (and Giratina), it'll just be the Lake Trio and Arceus as the Mewtwo role instead of being a mythical. Galactic plot would still involve legendaries due to how intertwined they are.
Cyrus summons Arceus through the Azure Flute and controls it with the Red Chain so you have to defeat Arceus (who you cannot catch at this point because Red Chain) and beat Cyrus. Then after you become champion, you can go to Celestic Town to get the Azure Flute from Cynthia or her grandparents to access the Hall of Origin so you can fight and capture Arceus for real.