I absolutely love this hack! The storyline is quite interesting. I did, however, find a few problems in Beta 2.
-Upon reaching Altomare, if you got into the Pokémon Center, and exit, you reappear in front of Salamence.
-Protagonist can't go back to your hometown upon reaching Altomare, but that could be part of your plot.
Anyway, your release of Beta 3 is one of the reasons why I should still be alive. Keep up the good work!