Just for the hell of it, I would like to see a different beginning; maybe not better, just different. It would begin with two young trainers as the protagonists, but instead of helping some scientist, these trainers would be brainwashed to work for an evil Team “Whatever” (the opposite of Plasma), and of course they would be the playable characters, male and female, you must choose one.
Team “Whatever” would be founded by Ghetsis himself, as a plan B for the possible failure of N, or as a countermeasure for the possible victory of N.
In the beginning these playable characters should be the exact opposite of the traditional Pokémon playable characters, that is some lean and mean evil cretins (as J from the anime), and rivals between themselves. They would wear some dark, sexy (18+ at least), sultry, outlandish, and skintight outfits as if they were some kind of supervillians, or evil secret agents, something as Marvel Comics’ Black Widow.
Their mission would be to travel around the world (in a sleazy, futuristic and black motorcycle, polluting the world, cause that is the evil way), to fight as many trainers as possible, to train their own Pokémon, and then to defeat all of the gym leaders of all cities, and elites in every region, and capture (or steal) every legendary Pokémon. That’s just the excuse to feature every character and pokémon and legendary pokémon already featured in past games.
It should be more focused in battles than walking around each route in the map.
And just for once, the starter Pokémon should be some other types, like dragon, bug, poison, dark, ghost or psychic.
At some point, maybe the lowest of your criminal life, you (your playable character I mean) would defeat N, so you can steal the legendary dragon of his (Zekrom or Reshiram).
At some other point, the greatest trainers ever would attempt to stop you, that means you must defeat people like Red, Blue, Lance, Cynthia, Alder, Professor Oak himself…
Trespassing the P2 laboratory to steal and activate Genesect, and finding and capturing Kyurem would be in your agenda as important steps to finish the main plot.
Of course, who would want to be the villain until the end? In the course of the game, the player would meet great trainers, wise people from around the world. Then your character would learn to really love Pokémon and to appreciate kindness in the people around the world, and maybe just maybe would be able to find love with another person. In other words, by the end of the game, your own playable character would change for good, so you can rebel against the people who brainwashed you, defeat the entire Team “Whatever” and ruin the most malevolent plan of Ghetsis.
Once finished the main plot, you could trash your villainous outfit and your evil motorcycle, so you can wear normal clothes and travel with a bicycle, now you are free to begin and enjoy a normal life, dedicated to protect Pokémon. At this point, the game would turn into a more traditional Pokémon game, that is, to explore and capture and breed and train Pokémon. And maybe build and fund a Pokémon Center by yourself, with Pokémon Hospital and Refuge, Pokémon Sanctuary, Pokémon Academy for trainers and breeders, and Pokémon Gym; this would give the satisfaction of building and managing something that many gamers like, and would give some positive use to the “hard-earned” money.
At some point, you would attempt to return the legendary dragon to N, but he would reckon your new and redeeming way of life, he would decide that you should keep the legendary dragon because this Pokémon itself has learned to love you, as you have learned yourself to love it as a friend.
In real life not everything is necessarily black or white, nor completely good or evil... there is grey, and there is redemption, everything is up to you, and you alone.