Pokemon Legends Hack Series Help Wanted!

I have a really cool idea for I hack series but i'm pretty new to hacking so i'm going to need some help. Also i need some help with the storyline so i need help with that. If there is a part of the storyline you think should change or that I'm not sure what to write comment and I'll change it if I think it is better a good change. If it is in ( ) that means I'm not sure what to put. Look down below for the story line and what I need help with at the moment.

The main storyline is that team Rocket, Magma, Aqua and Galactic have decided to join forces to once again take over the world. They drained all of the legendaries power. luckily it only turned them into baby form. (One of the professors) retrived a note that said "Go to headquarters in Isshu" The proffesors sent someone to follow a group of Rocket Grunts. The followed them to an uncharted island already full with native people and pokemon. They brounght back for pokemon which they found out were called Zoura, Tsutaaja, Pokabu, and Mijumaru. They also found out that Zoura elvolves into a pokemon called Zoroark with an ability called Illusion. Since they still dont know much about the region they are sending some older trainers to start their adventure there and find the new pokemon so they will know what's coming.Your job as a new trainer is to take one of the legendaries based of what region your in and raise it back to it's legendary form and defeat Team (IDK) and save the world! (Look below for each game and what i need help with)

Game 1: Pokemon Legends - Kanto

Heros:
You (You chose the name)
Rival 1 (you chose the name)
Rival 2 (You chose the name if i can get the help of a really good hacker)

Villians:
Team Rocket (or whatever the name will be changed to)
Giovaini (that's right he's back and badder then ever)
??? (there might be more)

Other People:
Prof. Oak
Your Mom
Bill
(Gym Leaders and Elite Four are still the same)
The Champion (???)

Starters (Types):
Baby Zapdos (Electic)
Baby Moltres (Fire)
Baby Articuno (Ice)
(The will be called something different like I think baby Articuno should be called Artica) (Also they wont be flying untill they evolve.)

Legendary Evolution Chains:
Baby (Legendary Bird) > (Stage 2) > Legendary Bird
Mew > Mewtwo (That's right they got Mewtwo too)


Other title coming later:
Pokemon Legends - Jhoto
Pokemon Legends - Hoenn
Pokemon Legends - Sinnoh
Pokemon Legends - Isshu

I like the idea! Cant really help, but I quite like the idea.

*Update* New improved story line to fit in with 5th Gen and to explain (not real reason) why the trainers are older than ever.