No exclusive events, I might add exclusive Pokemon at some stage that would be based off the character's name, but that would be pretty secret

Legendary Pokemon will most likely be added as boss fights, if you can get their hp low enough and inflict statuses and capture them without dying then they will be yours. Pokemon will eventually have drops like normal mobs, mostly Pokemon related things like berries and hold items which will go in Pokemon specific slots once tModLoader has UI hooks. One very special boss fight will yield a master ball, with a limit of 1 per character, kind of like the hard mode Demon Heart in vanilla.
It will be, and soon, I think I had better work on that for next version. After all I want to do the Pokedex in order and I don't have any of the evolutions yet...