Well, I never thought I'd be recommending fics for this category (since there seem to be many others who do more in this category than I do), but I actually have several! (And a tumblr link that has more general info about the author's specific AU (including how someone actually becomes a Pokemon Master!).
So, the author (of all of these) is
Skylight Sparkle, who has come up with
The Road You Choose. So far, the author has only done re-writes of Lucario and the Mystery of Mew, The Mastermind of Mirage Pokemon, The Rise of Darkrai, and Giratina and the Sky Warrior. For the most part, they start out as just re-writes that put Misty in the movies, but they're a HELL of a lot more than that, and the author has announced that there will be fics with a COMPLETELY original plot later.
I will admit, the Lucario movie re-write feels pretty much the same as the original, but I think the others have a MUCH different feel. (I think. The Lucario movie is the only one he's re-written that I've seen so far... XD)
As for links and summaries, here you go:
The Mystery of Aura - complete
Small things can bring big changes. While visiting Cameron Palace, Pikachu goes missing, and Ash, along with his friends and a mysterious pokemon named Lucario, go on a quest to find him. Along the way, Ash discovers things about himself that could change his entire life. AU Novelization of Lucario and the Mystery of Mew.
- complete
Direct sequel to The Mystery of Aura. Ash Ketchum thought that he experienced some strange things and faced almost every type of villain around, but this was something on a whole different level. One small thing can change everything, and sometimes the lines between what is real and what is just a mirage are impossible to see.
- complete
There's a balance to the world, a fragile but powerful one that keeps everything in motion. Something has started to shift and change that balance with potential cataclysmic consequences, and not everything is as it seems. This is barely the beginning, but for Ash and his friends, it might very well be the end. Sequel to The Master of Mirage.
- complete
Legends whisper of a world that is a shadowed, distorted mirror of our own. Should harm come to this world, the consequences to our world would be dire. Time and space aren't the only things on a direct collision course, but how a small little pokemon fits into all of this is a mystery. A very annoying one, if you ask Ash Ketchum. Sequel to Between Time and Space.
And, to go with Pokeshipping week, the author has:
Yesterday's Tomorrow - currently only the one chapter, obviously planning to release one more each day this week.
EDIT: The second chapter is now uploaded.
EDIT 2: Yesterday's Tomorrow is finished, I just never got around to editing my post...
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Author: [url=https://www.fanfiction.net/u/1631154/Skylight-Sparkle]Skylight Sparkle[/url]
[url=https://www.fanfiction.net/s/9346547/1/The-Mystery-of-Aura]The Mystery of Aura[/url] - complete
[url=https://www.fanfiction.net/s/10109906/1/The-Master-of-Mirage]The Master of Mirage[/url] - complete
[url=https://www.fanfiction.net/s/10286604/1/Between-Time-and-Space]Between Time and Space[/url] - complete
[url=https://www.fanfiction.net/s/10580126/1/Distortion]Distortion[/url] - complete
[url=https://www.fanfiction.net/s/10796789/1/Yesterday-s-Tomorrow]Yesterday's Tomorrow[/url] - complete