>>38640703honey trees are a shit mechanic. Headbutting and fishing is barely acceptable.
There are five main sources of pokemon, land, air, sea, ocean floor, and underground. Having encounters while flying was not doable in early gens, but in modern games it should be, as the hardware is powerful enough to display you flying over the land and through skies and shit.
Now have pokemon in an area change on time of day, season, and weather. This should cover most anything. Just do the math.
5 main areas
land, sea, underground, sea floor, air,
3 times of day
morning, afternoon, night,
4 seasons
summer spring fall winter
4 weather types
sunny/clearsky, rainy, snowy, normal/overcast
If you had lets say 4 unique pokemon for each permutation then any given area, land, sea etc. can contain 48 different pokemon.
