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After playing Pixelmon for a bit, I can see how several things from it could work into a full open world Pokemon game
>No random encounters, but random spawns of having around 15 wild Pokemon around you at all times
>Some Pokemon will start fights with you, try to escape, or downright ignore you depending on their proximity, nature, levels, species
>Pokemon have a ton of size variations
>All kinds of Pokemon can spawn anywhere in their respective biomes between a specific level range, you ought to choose your battles carefully and try to avoid higher levels if you dont want to get fucked
>Boss Pokemon that are ridiculously overleveled and oversized, which drop special items when defeated
>Moltres, Zapdos, and Articuno spawn after completing a sort of "quest" regarding their orbs like in Pokemon 2000