I've come up with quite a few ideas for Pokemon-based doujinshi over the years. Some of them I've stuck with, and will hopefully continue sticking with as I've gotten quite a ways into planning them out... a few others, however, haven't had much of anything planned out past the basic concepts. I could deem them canceled at this point, so anyone's free to take them. Here's one for now. I'll post a second canceled idea of mine later (two might've been all I had, but I forget).
I considered what Pocket Monsters would be like if it used a similar concept to Digimon Tamers: the real world is featured, right down to Pokemon being a popular media franchise, up until the monsters from said franchise start to manifest themselves into reality. Of course, Pokemon aren't like Digimon in the sense that they're living data that exists within networks, so a different approach would have to be used for the alternate worlds. In this story, I made it so that dimension-crossing is possible when an object represents one alternate world in the closest possible fashion, namely the data to a virtual game world. Pokemon are actually evil, territorial creatures that've been trying to claim another dimension for years. Psychic-type Pokemon, namely Mewtwo, act as their gang leaders because they were both able to confirm the existence of another world, as well as used their powers to slowly access the world. It all began several decades ago, when the psychic-types saw potential in our world's early development of computers, which could help form the perfect gate. They manipulated Satoshi Tajiri since his childhood (as well as others, like artist Ken Sugimori) in order to help create this gate.
Anyway, shortly after the perfected, supposedly final version of the Pocket Monsters video game (it would be a compilation game featuring all the regions and all Pokemon available up to the current generation... or, something new entirely if you wanna try making your own Pokemon, but that's something I'm personally against doing in my works) had just released, there had been reports of an amazing phenomena: upon encountering wild Koiking (Magikarp), players' DSes (or whatever made-up future portable) began to glow and open a portal that would release the Pokemon. People didn't make much of it at the time, and even allowed the Koiking to be introduced into the environment (they're not much of a threat to humans, though their occasional Tackle can hurt). However, over time, more Pokemon started to get through the gate, like early game bugs, birds, and rodents (the mechanics to the gate are similar to Yu Yu Hakusho: only weak monsters can get through at first, but over time, stronger monsters will start to appear as the gate widens).
The story takes place in some undecided district of Japan (more than likely Tokyo), not long after the Koiking started appearing (it's still being mentioned in the news, apparently). The protagonist, a teen-age boy, has sorta been out of the franchise since his childhood, with the original Red/Green games.... however, after much prompting from his friends (as well as an increased interest after the Koiking started appearing), he decided to get back into it with the new version. Upon starting his game, however, his DS also began to glow. Expecting another Koiking to appear, he instead got a distress message from Professor Ookido about the situation of Pokemon trying to break into their world (though, he might not explain all of it at first). After several attempts, humans finally managed to reach out to this dimension themselves, though only through a communication and transfer system. The truth is that Pokemon, being the terrorizing beings that they are, are usually hunted down by Trainers and brain-washed with the Monster Ball technology. Since Pokemon started appearing in our world, Ookido is concerned over the lack of Trainers, which is why he managed to establish a transfer system which reached out to a random DS. Because of the difficult of establishing this transfer system, Ookido has to ensure a trainer status to a single person for the time being, and thankfully, the protagonist accepts.
The trainer receives some Monster Balls (and maybe a Pokemon-tracking device), and before long, he captures a Poppo (Pidgey) without even having to weaken it. He's very fond of the Poppo because it reminds him of the very first Pokemon he caught way back in the day, which ended being on his main team (and likewise, in the story, it would've been his main Pokemon and eventually evolve into a Pigeot, which he would fly around the city). For some reason, I considered using some secret identity motif and have him treating this a bit lightly and overdramatize himself as a hero, sorta like The Great Saiyaman... but there would be a few problems to this (namely why couldn't Ookido have him inform his friends and have Monster Balls widely distributed? And why keep it a secret? In any case, I guess I liked the idea of Trainers being scarce).... I might've also made the transfer system one-way only for a while, giving the protagonist problems in early chapters when he has to find a place to store all his excess Monster Balls.
I had a few vague plots in mind as well... later story arcs would involve him running into other people who managed to be Trainers, some of which were evil (or environmentalists) and worked towards the Pokemon's cause (this story does seem like one of those "chosen warriors" type scenarios, but I always find it a bit cheesey when they're all inherently on one side and never have any conflict, if not being outright antagonists). The main character talking with Satoshi Tajiri about the situation would've definitely been used at some point, and an even later arc would've involved the trainers going into the Pokemon world (or perhaps the humans from the Pokemon world finally create a gate wide enough to get themselves through... or maybe both could occur, I don't know). The first chapter would've probably involved the hero (who already has his Poppo... his afforementioned background could be done with a flashback to allow the first chapter to get right into things) going to an apartment building that became overrun with bug Pokemon, which is probably the first reported situation of the Pokemon becoming an actual threat (Habunake might like this since he could involve Korobooshi, maybe turn one of his captures into a main team member). The first real difficult battle for the protagonist would come when one of the Koiking evolved into a Gyarados. I also had in mind for a hacker to get several Mew on his game only to end up releasing all of them into the real world later on (but then, if the latest games are supposed to be a perfect representation of the Pokemon world, why is Mew still unobtainable through normal methods? And why would there be more than one legendary in the other dimension? As you can see, I left a number of holes in these ideas ^^'... though, I kinda like the idea of legendaries NOT seeming like they're one-of-a-kind for once, which is probably why I considered it in the first place).
I think that's about all I had... with that, feel free to use any, if not all, of these concepts. Be sure to PM me if you do post it... though I don't usually read other people's fics, I might be interested simply because I came up with the concept.