I like how your starting locations changes depending on what you picked, definitely one of the more unique ideas! Don't think I've ever played a hack like that before. There's a lot of features you're planning on adding too, seems like it'd take a bit of time, but definitely worth it :3 Sounds great!
Sorry if this is long:
Most likely not going to make any headway on a hack anytime soon. Just throwing a preliminary concept out there.
The protectors of the sky, earth, and sea are Rayquaza, Groudon, and Kyogre respectively. At birth you are placed under one of the protection of one of these legends. Depending on which one you have (picked at game start), you will placed in a mountain region, island region, or land region. Everything is peaceful until one day Arceus decides to stir up a conflict among the protectors. Now with the three regions at war, it is your duty as the hero to gain the trust of your region and join forces with your protector Pokemon to take on the other two regions. Along the way, different criminal organizations of present and past stand in your way, including Team Rocket, Team Galatic who has taken control of Giratina, and Cipher with their Shadow Pokemon. Explore new lands while saving the world from devastation caused by the three protectors and other powerful forces.
Sprites from all generations
Revamped Map and Events
Day and Night System with Seasons
All Starters catchable
Starters for this game (depending on region): Archen, Kabuto, Shieldon
Legendaries from Gen 3 on catchable
Gyms replaced by Battle Arenas/Battle Frontier
Trade evolutions replaced by level up evolution
Afterstory including locating the variety of programmers (master AIs) and facing the trials given by Arceus.