Hmm, I've been thinking of a fan-fic plot regarding cresselia, darkrai and heatran, taking place in both unova AND sinnoh.
So the story starts with the female protagonist, who is a traveller and an experienced battlers. So as she was touring the Sinnoh region, she stumbles across Canalave City, where she hears a scream from a locked house. So then she later finds out, infiltrating with her Ditto, that the children was suffering from nightmares from Darkrai. Then suddenly, Cresselia appears with a holy light and motions the female protagonist forward, to pluck one of her feature to heal the child. The protagonist does so and heals the child, and then he gets cured and then the female protagonist revealed her name to the child's mother.
The scene suddenly flashes to Unova. A male trainer, who saw a Chanduelar heading into an abandoned mansion in Unova's desert region (BW2 reference) chases after the Chanduelar, with a strong desire to catch it. There, he meets a ghost, who lost her life from nightmares due to Darkrai. He retrieves a Lunar Wing in the house, which failed to cure the ghost's nightmares, and stuff it inside his bag, thinking that it was an antique. Afterwards, when he was walking on the Marvelous Bridge, heading back to Nuvema town, the feather shines and Cresselia appears. Only then, the male protagonist realised that there was people chasing after Cresselia, too, and was ready to, in any ways, capture it.
So it's practically a rough 1~3 chapters. The fan-made team appears and apparently, the leader controls Darkrai which goes around spreading nightmares and chaos, but Cresselia was preventing mass-nightmares to happen. The male protagonist's friend appears, and Roark and Bryon appears too.
Male Pro: Lanturn / Chandeleur/ Sceptile/ Ludicolo
Female Pro: Ditto / Cherrim/ Empoleon/Togekiss/
Male Sub: Dodrio / Scizor / Typhlosion/ Ampharos
How's the storyline?
I don't know. It feels like you're summarizing game events here. While a lot of writers attempt to do this, very few manage to pull it off because it's a pre-written story. You can expand all you want, but the baseline of the fact that it's still basically novelizing someone else's idea is still there.
That said, I'm not really sure what the storyline
is here. Sure, it's all about protagonists using Cresselia's Lunar Wings to heal people and something about a fan-created team launching a fairly generic drive to spread chaos as evil teams are wont to do, but... that's about it. There's nothing that ties the evil team plot to the female protagonist, for example, and there's nothing that ties the male protagonist's story to the female's besides Cresselia. You don't mention whether they team up or attempt to investigate/stop the team separately, there's no reason given as to why the fan-created team feels the need to spread chaos (because although canon sometimes likes to forget this point, doing something terrible just because you're evil isn't exactly the best motive), and there's nothing to note exactly how Heatran is involved. It feels like this is more of a smattering of concepts than a fully fledged idea or proposal, just because you've got a lot of different thoughts but not really anything that stitches them together. Try to figure out how to bring the characters together -- or at least try to find a way to blend all the elements you want to use into one coherent plot, even if that plot follows two separate characters doing their own thing (but going after the same goal in generally the same place at the same time).
Good luck, though.
In the Hoenn Region. Olivia (Dark type specialist who lives in Mossdeep as well.) takes over for Tate & Liza. (Bumped up to E4) and Wally takes over for Norman. Grass gym leader replaces Wattson (West meets him though).
Here I have to pose the first question: why the gym reshuffling? Note that in canon, gym types never really change, and there's usually a reason why leaders are absent. In GSC and HGSS, Janine takes over her father's position as gym leader of Fuchsia City because her father is strong enough to be inducted into the Elite Four (which makes sense because he's been training for years), but she never changes his gym's type. Likewise, Lenora leaves Nacrene City to devote more attention to the Nacrene Museum, but when Cheren, who has in BW wanted a chance to prove himself as a capable trainer, steps up to assume the position of Nacrene's gym leader, he doesn't change its type either. Usually, types are closely linked to the city, its culture, or the general setup of the gym. For example, the reason why Mauville has an Electric-type gym and not Grass-type one is because New Mauville, a semi-abandoned power plant, is located nearby. It's apparently part of the gym leader's duty to monitor it
and then send children off to fix it if necessary.
Generally, it might be a bit of a touchy subject to do a lot of roster reshuffling, especially if you don't present very,
very good explanations behind the new leaders. It's one thing to say that the current leaders were rotated out because of the five-year gap (because that happens), but it's another thing to say that the gym no longer focuses on the same type anymore or that random characters were promoted in the leaders' places.
Team Rocket returns with Giovanni as the leader, but as a force for good (unkown to people and they get attacked while trying to help at first. They wear white instead of black now also.)
Strangely enough, another member had the idea of turning an evil team into forces of good, and there's just a lot of problems involved in this. For one, while Giovanni ultimately surrenders at the end of RBY/FRLG, there's really no reason to assume he wants to get back in the saddle, so to speak, and lead, even for good causes. I mean, this is the guy who hid out in a
cave at one point in HGSS, after all, and the only reason why he left was because you(r avatar) figured out where he was. ...And even then, he was more inclined to lead his organization to take over the world again, had your avatar not stepped in and soundly kicked his tail.
Besides that, Team Rocket is a criminal organization -- a well-known one that has done things like take over multiple cities, abuse massive amounts of Pokémon, and hold people hostage. People are probably not going to like anyone who parades around and calls themselves members of the organization that, well, held them hostage and abused their Pokémon, even if the organization members insist that they're good.
But for more issues and lengthier explanations, you could always drop by
this thread.
Ghetsis is the main villain, but he has taken over Team Galactic along with Cyrus (who he claims as a prince)
...But they're after two different things. Ghetsis doesn't value anyone in particular because he sees them as tools to get at his ultimate goal of taking over the world. Cyrus doesn't think of himself as evil so much as
the solution to a problem. He's not trying to take over the world; he's trying to create a perfect utopia. It just so happens that he's delusional enough to believe destroying the world and recreating it to his specifications will be the means to that end.
In short, while Ghetsis could probably figure out a way to use Cyrus to his advantage, Cyrus would most likely not see Ghetsis as part of his solution because, you know, the whole "taking over the world" thing.
(Of course, this also ignores the fact that Cyrus is, according to Platinum canon, in stuck in the Distortion World, but I'll give you a pass and assume you're just going with DP canon and ignoring that Platinum exists. Because there are some writers who do that, so... yeah.)
they are going to try and control Kyogre and Groudon, later they also find out about Deoxys crashing in Hoenn and being researched at the Space Center and it they try to get him as an alternate plan.
While I can certainly see why Ghetsis would be interested in all of these legendaries, why would Cyrus? Remember, Cyrus is after creating a perfect world. He's not interested in changing the environment of this one. He wants to hit the reset button on the universe in order to eliminate things like human conflict and suffering -- things that won't be solved just by creating new oceans or new continents. Deoxys is even more irrelevant to his plans because there's pretty much nothing that it can offer to help further Cyrus's cause.
The heroes also run into former magma and aqua members… will they help them or cause havoc again?
To be fair (i.e., as a point in your favor), this is a legitimate question. Minor grunts
would be difficult to predict because some of them are actually thieves, while others seem devoted to the causes the organizations support. Once you get further up their structural ladders, however, you'll need more and more reminders that both teams are essentially ecoterrorists. They don't realize they're doing anything terrible; they're just like Cyrus, only with fewer delusions of grandeur. They have a plan but don't see how it could essentially destroy the world in the process. And they're passionate about their ideas and the belief that what they're doing is for the good of all life on Earth.
...But yeah, those low-leveled grunts tend to throw a wrench in those gears.
Also I’m thinking of having a side-fic or including in the story where they visit the Safari Zone and get trapped in with fossil pokemon which come alive and they have to defeat them, kinda like… Jurassic Park: Pokemon edition. Also maybe some other things have changed in the time that passed as well.
Try to tie together the main story before creating side stories for it.
As it stands, you talk a lot about changes but not really enough about the actual story. From your description, it sounds like West and Fleur's journey actually take a backseat to the war between all of the evil teams. (Just look at what you spend the most time talking about.) That in itself could make for a very interesting story if the motives for each team were straightened out.
The other half, West and Fleur's half, just feels a lot like it's an average trainer fic. Kids go on an adventure, start collecting badges, and end up entangled in a war against an evil organization. To be honest, I've always felt that these kinds of plots were rather weak because the author focuses so much on telling a story according to a formula that the formula doesn't really deviate. Looking at your summary, I feel like that's what's already happening. You have a potentially creative background idea, and that's what you talk about most here, even more than what West and Fleur are actually doing.
But mostly, like Oceanic's plot, it feels like there's just something missing that ties everything together, so you're right now listing a bunch of barely related concepts but not much in terms of a thread that connects each idea into one coherent plot. Think about what you want your story to
be, rather than what you want
in your story.