Here's an idea... Very strange... it involves Sonic Characters... (Namely, Blaze the Cat, Silver the Hedgehog, and Eggman Nega. {Maybe Marine too})
POKéMON Continuum Version
You play as either Blaze or Silver.
Eggman Nega has stolen the Sol Emeralds, and came into contact with Giratina, causing a tear in the Space-Time Continuum, thus warping himself along with Blaze and Silver to the Pokémon world!
Blaze and Silver wake up later in a forest.
Spoiler:
Blaze: Hnnn? Where are we?
*A random Pikachuu walks by*
Blaze: What in the...?
Silver: WOAH! COOL! A PIKACHUU!
Blaze: You know what that is?
Silver: I guess I'm not dreaming...
Blaze: JUST TELL ME WHAT THAT THING IS!
Silver: It's a Pikachuu.
Blaze: A Pikachuu? [... ... ... ... ...] Wait... isn't Pikachuu from one of those games you play?
Silver: Yes. I think we're in the world of Pokémon!
Blaze: Are sure?
*a Raichuu walks by, followed by a Ratatta, Starly and the Pikachuu from before*
Silver: That answer your question?
Blaze: *mumbles something under her breath* So... what happens in the game?
Silver then goes on to explain a typical game of Pokémon. After which he says they should try to get some Pokéballs... which are then thrown at them.
Random Trainer 1: Those are some strange looking Pokémon!
Blaze: WHAT!? WE'RE NOT POKéMON!
Random Trainer 2: RUN!!!
*The two trainers run off, Dropping some Pokeballs*
*Silver picks up the Pokéballs and gives Blaze half of them*
Silver: Blaze! Now we can catch some Pokémon! *He notices markings on one of his Pokeballs and one of Blaze's* ...And I think we got some their Pokémon too. Heh

'
Blaze: You... can't be serious. We should find out why we're here!
Silver: In this world, it's best we use a Pokémon to protect ourselves.
Blaze: You make a good point... I don't want to imagine what would happen if everyone in this world found out we where here and we constantly use our powers to attack their pets.
Silver: THEN LET'S GO!
Soon they reach the first Gym, and notice Eggman Nega's symbol on it.
It turns out that Eggman Nega has taken over (Name of Region) and the only way to defeate him is to deafete all 8 of his minions, take their Sol Emerald (one of them won't be holding one), and storm Nega's base.
Now for the twist:
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And I have another one! Guess who this involves... *pokes her theme*
POKéMON Shadow Version
You play as Shadow.
As Shadow was falling from the ARK at the end of SA2, he used Chaos Control... however, he wasn't totally able to control it, and ended up in the world of Pokémon!
Shadow wakes up in a forest (the "waking up in a forest" thing is getting pretty common these days...) and doesn't remember anything. (Oh how original)
He quickly goes looking through the forest and watches as a girl (Who, Oddly enough, resembles Maria) captures a (Insert Pokemon Here). She then notices Shadow.
Girl: Whoa! Hey! Cool! It's Shadow!
Shadow: Do I know you?
Girl: No, but I know you. My name is Mizura.
Shadow then has a flashback to watching Maria play a Pokémon game capturing the same thing Mizura did.
Shadow: Hm...
Mizura then gives Shadow the Pokémon she caught saying he should use it, and then leaves. (We don't see her again until much later)
Later on, Shadow defetes the first Gym Leader and finds a PokéGem (The Pokémon equivilant of a Chaos/Sol emerald) and hears of the legend of the 7 Pokégods, Of Purity, Continuation, The Sky, Wishes, Time, Space and Dimentions: Mew, Celebi, Rayquaza, Jirachi, Dialga, Palkia, and Giratina.
Also, a mysterious team known as "Team Hedgehog" is after Shadow for some reason...
He then decides to pursue the legend in search of answers.
Later on, Shadow collected all 7 stones, only to find out he needs the MasterGem to use the PokéGems. So he collects the last badge, and heads of the the Pokémon League...
Shadow defeats the Elite 4, and is about to face "The Master"/Champion...
Shadow soon gets the MasterGem, and summons Arceus...
*FIN* (Shadow is then found uncautious by Eggman, and... well, you know what happens next, right?)
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I dunno. I thought they where cool.