I do not really see evolution as something that should need a story, although I guess for continuity as Zeb said, evolution items should do. Im not even really for evolution items such as magmarize, dusk stone and things that would usually be found in another region as that would then fall under the same category as non evolution 4th generation pokemon. My main focus is the pokemon who evolve when they learn a certain move, so aipom, lickitung, yanma, piloswine, tangela (mime jr, bonsly). TMs are now possible so it seems to me a logical extension could be an item which say teaches ancient power or double hit and as a consequence causes such pokemon to evolve. It is evident that in the later pokemon worlds, travel between the regions is greater, and as a consequence the spread of new pokemon, new items, new moves to the older regions would be higher. In terms of PWOs storyline maybe the improvements in the train system meant that some traveller managed to bring these new items that teach ancient power to johto and kanto with the knowledge that they would cause these pokemon to evolve.
I would also like you to clarify again your point about not knowing what exists at all. PWO isnt set in the past, PWO is set in the future where communication between regions would be greater and so knowledge of other places would be common. I dont think it seems reasonable to think that each individual region would have no knowledge of everywhere else, what is found there and is in its own little bubble.
Maybe if you wanted a story for other evolution methods, maybe a convention of poke-scientists conforms every month or two to discuss the latest theories on evolution bringing stones from other regions and the like which people can purchase. Maybe make it so to gain entry to the convention, a kanto or johto scientist needs to quickly get a fire stone, or leaf stone, etc so he has something to present at the conference and if you get one for him he has a spare ticket. I dont know these are just ideas off the top of my head.