Mewtwo and Lugia are gen 1-2. They are in the files already and you will be able to catch them.there is a gym leader in ecruteak. You should try to search harder bro. For Mewtwo I heard that Pokemon3D has plans to bring in events that enables us to get pokemon that are not catchable in-game. And Lugia is probably in the whirlpool islands but that wasn't available yet.
Trapinch, however, is a different case. They will be implemented eventually, but in a different way. After Johto and Kanto are finished, they will continue making Hoenn (Ofcourse, if this project is still going.) and they will probably ''link/merge'' them and will make this game an all region Pokémon game.