Hmm. This is very interesting. As for me, my main change would be story, playing the same young trainer with a hat who becomes a legend is getting real dull. I think I may have a storyline in mind, however, this was mainly from my own game proposition so ignore the title:
Pokemon Amehyst Version- Cover Pokemon: Mewtwo (Plays a big role in story)
Story: You (either boy or girl version) are in a convoy on the way to a small town as a member of Team Rocket. Apparently a renegade legendary pokemon (You could probably guess who at this point) has been spotted within the caves of this town and your mission is to recapture by any means necessary. As you fill out your confirmation forms revealing your name and gender, you are then asked to choose your mission pokemon (Basically your 'starter') from either a Fighting type, a Psychic type, or a Dark type. The mission within the cave serves as the small tutorial of basic mechanics. Long story short, you and your two remaining teammates ( a boy and girl) make a devastating choice that affects the whole town to ruin, all for the sake of reaching the legendary. You confront it, but with your level 2 starter and the teammates' other weak pokemon against a level 45 legendary, things don't go as planned. Amongst all the chaos within, you black-out.
You wake up to a house in a small town and find a package by your side. The note introduces it's writer to Mr. P and according to the note, it has been one year since the incident and the town is still an isolated ruin. But since then, strange things have been happening to the world all starting with the scattering of 16 medallions amongst the sky. Mr. P proposes that the only way to make things normal again is to find all 16 of these medallions. The package contains the first one to show you what it looks which has engraving on it that looks like Mew.
Considering that you lost your original starter pokemon from the incident, you have to now choose another one from the lab in the town (This one being Grass-Fire-Water). After which, your journey officially begins.
Important Parts: In your journey you come across one of your teammates from before (Either the boy or girl depends on the opposite gender you chose). They quit Team Rocket and found a new group of Pokemon Rangers, and their goal is to redeem mankind and liberate all Pokemon from human influence (Though considering them being Pokemon trainers and rangers, that's really quite hypocritical). They ask you to join them and think about it. In another incident, you across the other teammate from before. He is still in Team Rocket and asks you to 'come back to the good ol' days' and think about it. Now the theme of the game is moral choice so the choice to whether rise the ranks of Team Rocket and use pokemon as tools or to join this new Liberation front and get rid of Pokemon help altogether (Basically pokemon 'hippies') is up to you.
As for these new medallions, these serve as the gym badges of the game, each engraved with a legendary pokemon in the series. The basis of most of the missions given from either TR HQ or PL HQ is to retrieve these medallions from their hidden shrines. The medallions are guarded by spirits of ancestors and they test you aka Gym Battle.
However, the theme of the game is Moral Choice. The choices you make in the game change the world within, from which towns are occupied by whom, which pokemon are available in your game, and what medallions you are able to retrieve. For example, you choose a mission to either twart Team Magma or Team Aqua from getting to the medallion first. The mission you chose makes you either fight the Ground type ' gym leader' to retrieve the Groundon engraved medal, or the Water-type 'gym leader to retrieve the Kyorgre engraved medal. So in essence you'll only obtain 8 medallions in the story.
There would be appearances from Jesse+James, Silver among others, including one girl you meet in the beginning who becomes a 'very important' character throughout the game, but I can't go any deeper into my story without some spoilers.
Features: Besides the moral choice theme, the game will also have an Alternate Way to Catch Pokemon. Unnamed at this point, this method is easier than pokeballs, but the captured pokemon is automatically disloyal to you at first no matter how many medals you've obtained. Another feature is customizable trainers. Along with cosmetic changes from clothes, trainers can now become specialized in a certain type and boost stats from that corresponding type.
And that's my Pokemon proposition, what do you guys think?