I want to have my say. That's the way Game Freak designed it, but there are a few little 'rules' about it. They didn't just put together randomly, so they had to follow some 'rules'.
- Notice how the starters are always the first Pokemon in the Pokedex? This is because they are the first Pokemon you will encounter in the game, most likely. From there you get the Pokemon that appear next/are more common than others, for example the Patrat family. The only time this 'rule' has been 'broken' is when they put Victini as #494 (or #000 in the Unova dex).
- By evolution. Obviously, if the Pokemon were introduced in the same Generation, their evolution chain will be close to each other, like Munna and Musharna.
- By Generations. Some Pokemon get evolutions in later Genearions, which leaves them stranded in middle of the Pokedex, far away from the rest of their pre-evolutions/further-evolutions. A prime example of this is the Eeveelutions.
- The Legendary Pokemon and/or the rarer Pokemon always seem to be at the end of a Regional Dex. Likely due to their rarity and authority power wise over other Pokemon.