If you really want your Pokemon for the new save file you could trade them yourself if you have access to a second PC, or you could ask a friend to transfer them to him and then back to you in your new save. Remember there's also the new online feature and you could get Gastly or any other Pokemon by asking in the Online Play thread.
And about the changes, Ep. 16 has a new reputation system, in which you get positive or negative points with characters based on your choices trough the game. As of now these points don't do anything, but they most likely will in future episodes (Ep. 15 saves don't get these points).
Also you might get to find new stuff you missed in your first play trough, so if you really like the game I would say it's totally worth it to start over again.