>>493712531. Legendary trios being prefered to quartets or quintets
2. They designed it, but they weren't satisfied with it, so they scrapped it. This is the most likely explanation.
3. They started out as cardinal directions but were replaced with North American weather kami (Thunder, Tornados, Earthquakes)
4. Odd numbers were preferred to even numbers because Odd is male/yang.
5. "Tornadus and Thundurus were initially red and blue in color, but were changed as they clashed with Sawk and Throh, who were also designed after Oni. In addition, Landorus was added later when a change was made during development, suggesting that the Forces of Nature was meant to be a duo as opposed to a trio.[1]"
6. Same as the above theory, but the 4th was scrapped so late in development that they didn't have time to create a new one.
&c. &c.