Just an fyi, but those episodes are edited for presentation to mask the jump cuts to edit saves / changing of ROMs.
You currently cannot change starters, but you can swap animations of a 'random'ly chosen pokemon to overwrite Treeko, Torchic and Mudkip.
You can't force shiny encounters, but you can swap textures to have a normal pokemon use its shiny texture (temporarily), then edit the save file after you catch it to make it shiny.
You can't change the storyline, but you can change text and swap ROMs so that NPCs say things at different times.
etc.
However, you can modify your ROM with any of the pre-programmed randomizer functions with pk3DS.