I started remaking the beta when you reported that glitch and I hope it won't do the same.
Some changes:
Prof. IKE will be your father,he won't appear in the intro,his lab will be in Silon Passage
Start in a cave where you won't get there again,WARP HOUSES and CAVES are deleted,I added train stations :D and a Truck Guy,in the cave you start there will be an earthquake that Team Tornado caused,you'll go in ur house (always the left one) and wveryone will be safe then,your father will give you your first pokemon so that you can be safe in case Team Tornado attacks,and more...