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This thread is six years old but where else are you gonna throw out random ideas, huh?
I was playing through Shattered Dimensions recently, and (spoilers for that) there's a part where an NPC speculates that the heavy snowfall is caused by a Pokemon. When I saw the alternate dimension was sunny, I thought that it was going to turn out that in one dimension, there was a stand-alone legendary like Heatran causing the snowy weather, and in the other, a different legendary that fit the same role in the story but with a totally different legend and powers. I got to thinking about what that might look like with some of our canon legendaries!
Mew/Mewtwo - Switch their roles with Arceus and the Type: Null line! Gladion escapes the Aether Paradise with a grumpy cat in a clunky helmet, who evolves and can learn every move through the M.E.W.v2 System, while in Cerulean Cave, a horned creature with the ability to change types hones its powers... (And if you believe in the "Ditto is a failed clone of Mew" theory, maybe Cinnabar Mansion has curious little deer scampering about with Color Change as their ability)
Legendary beasts - Three Pokemon were killed during the creation of the Brass Tower - a Grass-type, as wood was cut to build it, a Ground-type, as the foundation was being set, and a Steel-type, as the brass was being melded. It's said their spirits still haunt the tower's floors, though the tower's guardian manages to keep them confined within...
Regis - Five artistic Pokemon collaborated together on a masterwork, a mosaic-like golem with traces of each creator within.
Lunar Duo - A lunar trio, with a gibbous, a half moon, and a full moon Pokemon! (not sure what they'd represent - non-REM sleep, maybe...?)
Lake Trio - Three Steel-types based on Asimov's laws of robotics - one for obedience, one for self-protection, one for protecting humans.
Swords of Justice - A Dark-type group based on some famous villain team instead!
(I guess this isn't really "fitting the same role in the story with different powers" so much as "having a different story entirely", haha)
One idea that I had for a game before settling on my current project was that each town/city is a horror-story in its own way with a mystery to solve in each one.
It eventually leading to the reveal that the entire region has fallen under the spell of Darkrai who has been captured by the villains and that by solving the mystery in each town, the player is coming closer and closer to escaping the nightmare and setting the region free.
I had two little ideas for my game (that I don't know if I'll ever do because all I have been doing is adding mechanics I want to include and nothing else).
The first idea is that there were (or are) temples in the different towns of a region led by a kimono girl (or any other figure of authority that fits the game and theme) and they would hold trials for people with pokémon. The trials could be for many reasons, like testing the bond and strength of the people and their pokémon (like the gyms and the Alola trials); as a rite of age, so that the young could probe if they have become adults; as a test to see if the person in question could bond/see the legendary pokémon the temple worships; maybe even as a test to see if the person doing it was apt to become part of the temple.
The second idea is that there are centres (or simply people) that hold tests for travelling trainers who do not participate in the pokémon league (or the equivalent for the region) as a way to let them use field moves outside of battle and/or let them have stronger pokémon without them disobeying.
Edit: I saw after I posted this that this is to share ideas one isn't using for their game. While I still have the idea of using the above two for my game, I thought of leaving them here since I'm doing practically nothing to actually make my game nor do I know if I'll end up leaving those two ideas in my game (neither is the main plot, just side things the player could do).
One of the main villains is a subversion of the usual rival/friend who's mysterious at first but has a sad backstory, who befriends the player over time, has a garbage parent and leaves the region. Except here, said character is the main villain for 2/3 of the story, and their parent is a faller in the current day, remembering nothing about their former life or family. When he leaves the region by the end, it's ambiguous whether he's alive or not - all that matters is that he's finally free of the vendetta that poisoned his life, and that he can be together with the love of his life no matter what.
The postgame is a conclusion to the story of the Aether family from SM, with Lusamine tending to other fallers, and helping the International Police catch Ultra Beasts to make amends for her past crimes. Even after being sick in SM, she struggles with the aftereffects of the neurotoxin, and comes off as a struggling, selfish addict. We find out Gladion stopped being president out of burnout, that Lusamine lost custody of her own kids after her misdeeds were revealed to the public, and that Whitney's Miltank stopped Lillie's journey cold in Johto. Over the course of the story, Lusamine grows even further out of her own flaws, and reconciles with Lillie and Gladion, letting them go on their own terms.
In contrast with a former female villain redeeming herself, the real villain of the story is a female clown from who knows where with magical abilities, pulling the strings of everyone in the story to conquer and destroy the world. Comical yet sociopathic and sinister, the idea was to make her Pokemon's answer to Kefka or Dimentio
I had a really fun idea a few years I ended up scrapping for a prequel to Pokemon Black and White or possibly a re-imagining of its lore
You take a personality quiz to determine whether you play as one of two princes/princesses
The Black prince/princess is in favor of the burgeoning sport of Pokemon battling and wishes to make it widespread so the people can use it to find their place in society through their skill with the support of the great dragon
The White prince/princess wishes to ban pokemon battling so people and pokemon can continue to live in harmony and wont uproot social norms with constant social mobility with the support of the great dragon
The Black prince/princess's starter is Seviper and the White prince/princess's starter is Zangoose. The great dragon refuses to work with either of them unless they gain the support of the people so the two both set out on a quest to earn the people's support with the one you don't play as being your rival.
I had a lot of fun imagining scenarios with this concept but I don't think I could write this kind of story with a chaos/law dynamic when I'm just a bit too biased towards chaos.
Zangoose and Seviper are the perfect starters for this kind of game since they're also white and black eternal rivals defined by their conflict with each other just like Reshiram and Zekrom.
I have a history of my fangame ideas involving these two as the mascots since I had another fangame idea even longer before this where the player had Zangoose as their starter and Seviper was the main villain's ace and even now, the game I'm working on that I'm determined to finish has the player use Seviper and Zangoose as their starters like how in Colosseum you start with Umbreon and Espeon. I just can't get these two out of my head.
Is it an idea to allow certain two species to breed into a whole different species? For example, if specificly Bulbasaur and Charmander breed, there's a 10%? chance for a Squirtle. That's dumb obviously, but would the mechanic be interesting?
It's that game people dream of but never accomplish - a game with every region! Choose where you begin, and get your starting Pokemon based on your starting region! How did the developers manage it?
Well, simple: there's nobody but you. This isn't a "conquer all the Pokemon Leagues" game, it's a horror(-esque?) game where you've woken up to find you're the only person in your hometown, in your region, maybe even the whole world? And you've set out on a journey to find out why, or else try to find what life you can make in such an empty world. Maybe this is one global catastrophic event, or maybe the disaster changes depending on what region you play through. (Maybe Alola's is the Guzzlord attack that caused the Ultra Ruin, maybe Sinnoh's is Cyrus' perfect world, or a nightmare created by Darkrai)
(Nice thing about this premise - you can lock doors or destroy buildings to cut down on maps, and you don't have to worry about populating places with NPCs, lol)
Gameplay is mostly just wandering about the empty world, trying to find clues - maybe scrawled messages in buildings, or more subtle environmental storytelling. Maybe you rarely battle, since there's only wild mons now, maybe you have to scavenge for supplies, or add PLA crafting mechanics.
Your "starter Pokemon" are a set of HM mules specific to the region, with a complete set of HM moves. I was playing through Platinum when I thought of this, so, Sinnoh mules -
* indicates a move that wasn't used in the original region
Staravia
Fly
Defog
Bastiodon
Strength
Rock Smash
Dig
Headbutt (just for the sake of having more field moves)
Bibarel
Cut
Rock Climb
Surf
Waterfall
Whirlpool*
Dive*
If you give Bibarel more of the water-transport moves, maybe give Cut to Staravia and/or Rock Climb to Bastiodon
A Medicham could fit, too - Flash, Rock Smash, and maybe Teleport. (It doesn't learn it in canon, but it'd make sense)
The default party in Essentials is actually a Kanto-based team with every field move, so that's taken care of for you.
And one more party just for the hell of it -
Swanna
Fly
Surf
Waterfall
Dive
Whirlpool* (it's never learned it in canon, but it'd make sense)
Defog*
Excadrill
Cut
Dig
Strength
Rock Smash*
Rock Climb*
Golurk
Fly
Dig
Strength
Rock Smash
Flash*
Completely changing gears - the colors orange, purple, and silver are notable because they don't rhyme with any other words in English - could be a fun little touch for a legendary trio? Not the whole basis, of course, but like, a little trivia you notice about the design, like how UBs all have prime number base stats
A few villainous teams have always seemed a bit strange to me with their grunts. Team Plasma, Team Aqua and Magma, and Team Galactic all have this talk about their goals being for the bettering of humanity, but their organization is structured like the obviously-evil Team Rocket. Galactic kinda gets a pass because their grunts could be swayed by the idea of getting a better place in the new world, but I felt like that wasn’t as much the talk with Aqua and Magma? Maybe I’m misremembering. It’s definitely not the case with Plasma, although if Plasma’s the only exception then it could be argued that the grunts thought it was like, a parody…
Anyways, my point with all this is that I think it’d be interesting if teams weren’t exclusively villainous. Maybe there were already little teams out in the world just pursuing pet interests, and the others seem more normal by comparison. Team Nature gives their Rangers gear all the time, should we really be that worried about Team Aqua’s uniforms? They’re just like, the ocean environmentalists, right? So what if there’s a big Team Galactic Warehouse? Team Gamer runs an arcade.
This next idea was going to be one of those teams, but probably makes more sense as just its own thing-
Those TMs the player finds in the overworld, sometimes in thematically-appropriate locations? Yeah, they’re not just the player being extremely lucky and always a finder, never a loser- they’re an intentional advertising ploy from the company that sells TMs to marts and arcades. Tough trainers using their cool moves draws business - that’s why they have contracts with gym leaders, after all- and the trainers going to these dungeons are the best of the best!
Of course, the poor employees set to leave them out aren’t always up to these battle standards at first… But hey, a bag full of TMs and risky challenges like these tend to make strong trainers, right?
I think it depends on what species are involved. With most Pokemon, I think it'd seem a little strange-it's not like crossbreeding in real life results in a purebreed of another species, after all-but there are some cases I think it could work. There's the obvious example of Type: Null, but there's some other Pokemon it could make sense with, too. Like what if you bred a Chansey and a Driftblim to get a Jigglypuff? (Course, you'd have to move the egg groups around for that)
Long time ago I thought about this. The Dragon Warrior Monsters (my favourite Game Boy Color game) do this very well (in my opinion). There are 10 family/types (11 in sequel), and every type combination generate a specific monsters (table), plus some specific cases. If you breed a Bird family with a Zombie family, it will generates a Bird MadRaven. If you reverse the order, it will generates a Zombie RotRaven. If you breed a SabreMan (a sword) with a SlimeBorg (cyborg slime), the egg will be a Roboster (robot with a sword).
This sounds something doable in fangames, maybe with breed groups instead of types.