Ideally adds all or most. Recognizes some possible barriers with that (updating movesets, abilities, model creation and testing, behavior). Aims for at least 10-12 evolutionary lines of each Pokemon type catchable in both games. Favors Pokemon with the fewest number of appearances in-game (by main story, not by transferability).
Also needs to consider biome population. Is there a good variety of Pokemon in grasslands, caves, deserts, oceans, and snow areas? Feels bad if there are new Pokemon are every turn in the grass, but only swarms of Zubats, Geodudes, and Drilburs in caves. Results in higher numbers of Water-types, probably.
Technically needs to consider power distribution a little too. Might have lots of non-evolving Pokemon planned for an early biome or something. Imagine Pinsir, Heracross, Tauros, Sawk, Throh, Durant, Bouffalant, Stonjourner, and Indeedee in some hypothetical early biome. Invalidates the point of all the quick evolution Pokemon (even more). May need to cut certain Pokemon (and reintroduce more common ones) out of balance.
Edit: Restricts legendaries to 10 or so: 2 box art, 0-1 big bad, 3-4 of a theme, and 5ish for fun cameos/callbacks.