Hack the PC system and release everyone's mons, and maybe make it so no more can be put in ever (until someone counter-hacks it). Pokemon currently with their trainers would be unaffected, but you don't get everything you want at once.
My plan wouldn't really be any sort of evil conquering, more like massively trolling every single Pokemon trainer out there.
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Kidnap all scientist and professor. Then make them develop a device that can make people create its own pokemon easily from the scratch like how will it looks like, type, ability, attack, gender etc. That way everyone simply can make their own "generation" pokemon