Everything will be very interesting when we are able to send the R/B/Y mon over. I hope they add also certain egg moves because with certain moves available as TMs on these games, it would be a shame if could not breed them over to other gen mon.
Natures , abilities , etc will probably be determined in a similar ways shiny and gender were determined when transferring from Gen I Gen II. They probably just found a way to successfully transfer from that IV system to the current one finally.