1) Based on Pokespe, in terms that only a select few posses a Pokedex. The original Pokespe characters would all be in their twenties and be famous. (moreso than they are already) as well.
It is about a brother-and-sister team. The boy, Hematite, is in a wheelchair, and Garnet, the girl and older sibling, would like Hematite to become a Pokemon Trainer as well. The idea is that a year before the present day, Garnet said she would go on a Journey across Hidem, my made-up region. Hematite is jealous, thinking that just because he's wheelchair-bound he can't ever be a trainer. (Or so says their grandparents, whom they live with.)
What Garnet was really doing, was planning a path for Hematite to be a trainer. On Hematite's 11th birthday, she gives him two Pokemon- a Ponyta (or Rapidash) and a Buizel. Her idea is that Hematite would ride on Ponyta when the Wheelchair is not plausible, and that Buizel would be his Starter.
So basically, Hematite and Garnet would travel around Hidem, with Garnet being Hematie's 24/7 guardian. Oh yeah, and there's probably going to be some crazy take-over-the-world scheme going on. (not sure what or why or how)
I'd say go with this one. It's an idea that isn't basically average new trainer faire, and it deals with subjects that could be potentially interesting. You also have fewer problems with this one than the other one (which I'll get into in a moment). With this idea, though, you'll want to take into consideration two things that you haven't really described above:
1. The fact that Hematite is disabled. A lot of newbie writers tend to give their characters interesting obstacles to face (blindness, psychological disturbances, that sort of thing) but forget to follow through with it. Don't forget that your character ultimately can't walk, and this will most likely end up being a problem later, even if he has a Ponyta. It will probably affect him psychologically (especially since he's been told all his life that he can't do certain things that a lot of other people in the world can) as well as on the obvious physical basis.
Also, try to think about
why he's in a wheelchair. Sometimes, being in a wheelchair doesn't just mean not having the ability to walk, depending on the problem that led to the character being put in one. Cerebral palsy isn't the same as paralysis caused by an accident, for example. Either could bring in a whole list of other problems for both the brother and the sister.
In other words, yeah, I know it's one of my most-stressed pieces of advice, but remember to do a bit of research before going into this kind of character. It can be well-done if it keeps in mind that the wheelchair means a whole lot of things to the character.
2. How this relates to Pokespe. Right now, ignoring the part about Hematite's disability, it seems a lot like an average journey. Pokespe, meanwhile, tends to be about kids who are destined to save the world from legendary-related disaster. The journey (badges, ribbons, et cetera) tends to be a side quest, sometimes even explicitly so. (Looking at you, RS arc.) Normally, it's kosher to have a story set in a canon universe, but because this is set in a fan region so far into the future, you'll want to make sure the reader knows that it's not a fic based on the franchise in general but instead one based on a specific universe. You'll probably have to bring in elements of the stories in Pokespe and bring up the characters, depending on how you want to establish the story's setting. (You'll probably end up having to bring in the stories from the canon universe anyway because, heck, they
saved the world on multiple occasions.)
2) A more simple story. This one would be based on my adventures in the games, but not necessarily the games themselves. (if you follow) Basically, it would start off Hoenn and then go to Sinnoh, and then Kanto and Johto! (I may or may not include Isshu and future regions... it would sort of depend on where the region is)
Basically, most of the core plot would stay for the most part. However, there will be some twists...
Also note, that I would wish to use Japanese names for all characters, locations, and Pokemon. Moves and Items would still use their English names.
Since this is BASED on MY adventure IN the games, the continuity in the games is semi-ignored (Basically, the events of Kanto are never seen, and rather, Momoko would go through the HGSS Version (not the GSC Version), with another rival having been through the original Kanto.)
So basically, what Momoko wants is to be the best damn Dragon-Type Trainer ever. (She Idolizes Clair/Ibuki and Lance/Wataru)
I actually have to do this in list format.
1. While you said Isshu's presence in your story is a maybe,
never include a region in an upcoming game in a story until more information is known about it. The reason why is because if you know very little about it, you'll end up having to speculate, which means that when the actual games come out, the details in your story (Pokémon in your region, how moves work, what moves each Pokémon will learn, what kinds of places and gyms are across the region, that sort of thing) will probably be all wrong.
2. Unfortunately, while you have the bit in the spoiler tag about Team Magma, the rest seems to be generic new trainer faire. You've got a girl on a journey to become the greatest trainer (even if it's just with Dragon-types... which actually raises a completely new issue I'll get into in a moment). She's probably going to go on a badge quest of some kind, and she has her own generic rival. Not only that, but you've also basically said that this will follow the games. (Only... not?) So, it'll probably be a little less exciting than your first idea because this kind of thing, where the embodiment of the writer's game character sets off across a region to collect badges and go through the basic plot of the games, has happened quite frequently in fanfiction anyway.
3. I can only wonder what kind of starter she'd have, considering Dragon-types are extremely rare. They also tend to suck early on but grow into serious powerhouses (which means you'd probably see her taking on Johto without too much trouble if she's got a Salamence or something), but mostly, they're just intensely rare. Some of them tend to cause the reader to laugh if you bring them out. (For example, if your character starts off with a Dratini she finds in the wild -- especially
injured in the wild -- this will probably cause your fic to be considered a parody because so many parodies start off like this anyway.)
4. I cringe a little at the occasional disregarding of canon. I mean, this is either based on the games, or it isn't. And even then, you'll probably run into problems because some readers will expect that certain canon details (like the entirety of the Kanto plot) will pop up when, in your story, they won't. In other words, your trap is the fact that this sounds a lot like standard new trainer faire, and it sounds like you're basing this on the games (sort of). As a result, a reader will end up assuming that they'll be following your character through the basic plots of each region, and when they don't see them, they'll wonder when this story is supposed to take place.
This will probably get even more confusing because of the way the timelines in each of the games work. RBY/FrLg and RSE are set in the same timeline; DP and GSC/HGSS are set in a timeline three years
after the first one. In fact, HGSS's Team Rocket subplot happened
because of what happened in Kanto three years prior to the game's events. So, to say that Kanto's plot happens at roughly the same time as Johto's just invites a mess because the Team Rocket in Johto don't have a reason to screw around with Magikarp in the Lake of Rage or take over the radio tower in Goldenrod yet.
Not only that, but the bit about Wally seems like there's no reason for it. I mean, the entire point behind why he hangs out with the player character is because he got his first Pokémon with their help thanks to the fact that his family didn't want him to leave home. As in, they thought he was too sickly to go out on a journey, so they wouldn't give him a Pokémon. In the games, at least.
5. There's also no difference between GSC's core plot and HGSS's. The differences between the games are in the features (including where you find Suicune), side plot (like the Safari Zone stuff), and the role of the kimono girls (which seems more like a superficial thing, really). Just so you know.
6. While I have no problem with writers using Japanese names for characters, locations, and Pokémon (and, in fact, one of my favorite fics does this), it really has to be all or nothing for the sake of consistency. As in, it wouldn't make sense to go with Japanese names for three elements of Pokémon canon but English names for the rest. Your readers will probably end up having to look things up
anyway because most people don't know every single character's Japanese name. (For example, if I said Mayumi, I'm not sure how many people would know who that was right off the bat. They likewise probably wouldn't know what Hajitsuge or Taneboh were. So, they'll probably have to look those up just as much as they would probably have to look up Kougousei -- or, if I wanted to make things easier, Photosynthesis -- or Orennomi.)
7. Finally, you'll probably have trouble tackling this kind of fic. While it's not unheard-of to create a fic that spans hundreds of chapters and multiple books, keep in mind that to write a good epic like those will usually take years of work.
In short, yeah, you'll probably have less trouble with the first one. Good luck!