At the beginning of time, there was Arceus. She created all that is in the universe and created the creation trio and the lake guardians. Palkia and Dialga conceived a child who had the power of all Pokémon, but their deteriorating relationship forced Arceus to move the child to a future date where she would be able to lead a normal life. Just to be safe, Arceus locked the child's form to her human form, made it so she couldn't use her powers except for the ability to break ties from a Pokemon to a human (ie. freeing a Pokemon from it's Pokeball), and her ability to understand Pokémon.
The girl, named Dulcinea by her foster parents, leads a normal life, aside from having Pokémon swarm her a lot (due to her legendary status), going through elementary, middle, and high school (at age 10 they begin their education in learning how to care for a Pokémon but are not considered eligible to own one yet) in the Unova Region. She elects to go on a gap year (which lasts two years) with her two friends, Jackson and Emily on their Pokémon Journey (which is part of that gap year. Theoretically, the gap year was supposed to be a journey of exploration, to find where one belonged in the world before settling down into an occupation but it ultimately devolved into challenging the Pokémon League in many cases). After their graduation, they come across a Zorua being abused by its trainer.
Inexplicably, the Zorua is freed from its trainer, who is quite angry about it and is about to strike Dulcinea when he gets kicked in the balls by Jackson. When they go to Professor Rowan's lab to get Jackson's Pokémon, the Zorua tags along and wants to be Dulcinea's Pokémon. After the whole assault and battery thing is worked out dealing with the abusive trainer (the laws against it are a lot tougher in the Pokémon world aside from the fact that abusing a creature that can wield supernatural powers is an incredibly bad idea), Professor Juniper agrees and they go on their journey, Jackson having chosen Oshawott as his starter.
Progresses much the same as the game, with Dulcinea slowly realizing her lineage. In Lumiose City, they meet Cynthia, who relates to them the part of the legend where they mention Dulcinea. She realizes that she looks a lot like that Legendary Mon's human form. One night outside of Anville town, she begins to have terrible pains and leaves her tent. She transforms into her Pokémon form. Her transformation wakes up both Jackson and Emily and they go out to investigate. When they do, they find Dulcinea and are shocked at the sight of the legendary child of Dialga and Palkia. Jackson immediately attempts to capture her, but of course the Pokéball just lands dead after contacting her. Dulcinea can't physically talk in her Pokémon form, but trying as hard as she can, she manages to reach out to both Jackson and Emily, letting them know who she really is.
After going through the whole, "If you're really Dulcinea, prove it," phase by revealing embarrassing details about Jackson that only their trio would have known about, they begin theorizing about what it actually means, especially in relation to the legend. They come to the conclusion that they are the ones who are expected to save the world and are freaked out about it. For one thing, they don't know who the person who will threaten things is. Dulcinea is especially worried because she doesn't want to have to leave her friends. The story continues apace, discovering Team Plasma is the group they are bound to oppose and just how messed up their leader is and their plan, to enslave all the Pokemon so they can take over the world as well as find the source of the universe, the remnants of the egg of Arceus, until the time they reach the castle where an epic battle between Ghetsis and the chosen heroes occurs involving Reshiram, Kyurem, and Zekrom.
In the end, despite grave injuries on all parts, they win the fight. Freed of Ghetsis' control, Kyurem drags Ghetsis off to Giratina so he could be thrown in the distortion world while Dialga and Palkia arrive and have a heart to heart conversation with their child. She yells at them for having abandoned her when she was a baby and they try to explain why they had to do what they did. Ultimately, this ends with Dulcinea going with her birth parents to the Hall of Origins where she was born.
Of course, she does not do this voluntarily, only having gone out of a need to be healed by something stronger than a potion or what a Nurse Joy could do after suffering near life threatening injuries during the battle. Her parents then force her to stay as the prophecy did not mention anything beyond returning to the Hall of Origins. Jackson and Emily, heartbroken over the Legendaries taking the one he loves and the one who is her good friend respectively go on a quest to obtain the Azure Flute, ignoring the fame and fortune that came from saving the world from the apocalypse in an attempt to reach his girl.
Dulcinea, in the meantime is taught by several of the Legendaries how to control her powers and is told to forget Jackson because of the fact that he is mortal, that he will eventually die and she will be forced to leave him. She responds that the whole concept of death in their universe is merely a transitory stage to the world that Giratina rules, and she could simply go and visit him there.
In the meantime, over innumerable dead ends and false leads, Jackson and Emily finally find the Azure Flute and call down the path to the Hall of Origins. When they get to the top of the flight of stairs, they find that the Legendaries are willing to let them in, but are not to see Dulcinea. Jackson says, "To the distortion world with that, Legendary or not, we came here to find Dulcinea, and damn all who get in our way." With that, a grand fight begins, both with Dulcinea fighting to get to her friends, and with her friends fighting to get to her. They at the least get into eye contact with each other, but then Arceus ends it, holding everyone in psychic holds. She chastises Jackson for his choices, and tells Dulcinea that there is a reason that they tried to keep her from Jackson: It hurts to form bonds with the mortal people because they will eventually die and disappear into the aether, hence the distance Legendaries keep from people, which stems not only from hate of those who would attempt to enslave them but also from the pain of losing loved ones when you will go on forever.
In the end, she allows Dulcinea to return with Jackson and Emily, but only on the condition that she continue to train and that she be aware of her friends limited lifespans.
Unova, although undoubtedly based on America would probably have a rail system (Anville town) based on the British rail system (unless there is more to the landmass Unova belongs to than the region shown, which is implied by the image of Unova from the game globe) meaning that the trains used are more for passenger work as opposed to hauling large amounts of freight great distances, like it is in America.
Unlike Britain though, the loading gauge is strong enough to take trains from America, so if it had to it could take trains from railroads based on America. So, the main model of passenger train would be based on the British Rail Class 91 with the first electric locomotives being based on the ES1 locomotives which would have been used for shunting.
In terms of Diesels, the Class 67 would be the main freight hauler, with the Class 55 being a mixed freight locomotive used in the past.
The trains that the line used prior to that would be based on the trains of the LNER with rolling stock from all four of the big four railways depending on the type of freight they were hauling. This would mean that the main passenger locomotives of the main line would be based on the A3 (Flying Scotsman) and A4 (Mallard) locomotives of the LNER, with the long haul heavy passenger trains being carried by trains such as the P2 Gresley locomotives as currently designed by the A1 steam locomotive trust.
The main freight locomotives would be based on the LNER P1 and the LNER B12 class locomotives. The main branch line locomotives would have been C, J, and K class tender locomotives. For shunting, the railway would have used smaller locomotives such as the E2 of the London, Brighton, and South Coast Railway as well as their own J and F class tank engines for light stuff and the Wordsell Class T1 and the A8 class locomotives for the big jobs.
As for the aircraft, the models would be based on American models, in keeping with the theme that the United States is the basis for Unova. The runway system at Mistralton city would most certainly not be that short for a major import/export cargo hub and would most certainly not have a hangar at one end of the runway. The runway system would make more sense shaped similarly to O'Hare International Airport. The gym could still be in a hangar, but it would have to be one not actively used.