Since modern Pokemon games focus on legendaries, here are some ideas for how Gen V could have gone:
This idea is what we have now. Reshiram and Zekrom embodying Yin and Yang, and Kyurem embodying the void.
Clear would have N getting both Reshiram and Zekrom, and you having to go get Kyurem to fuck their shit up.
These would focus around Dennis. Since Team Plasma supposedly created him, wouldn't it be nice to, let's see... PUT HIM IN THE FUCKING PLOT? But no. He's an event legendary. WAY TO DROP THE BALL, GAMEFREAK.
Basically, both games would have their own Dennis, with vast differences. N could use Dennis to meet his goals, and when he realises he's wrong, he gives you Dennis, as you're the only one who can actually use him without destroying the world.
These would focus around the Musketeers. The original three versions would each have you riding in on your own Musketeer, and there would be two teams each with their own legendary. The one you get depends on your version, and the team that helps you depends on your version. The ultimate goal is to get all three together, so they can undo the damage they caused. Cream would have all three teams trying to destroy eachother with their legendaries. You have to get Keldeo to destroy them and reunite the three musketeers, adding to them the fourth member.
These could be R/S/E rip-offs, one team wanting LIGHTNING STORMS from this fucker, the other wanting TORNADOS from this faggot. Of course, you'd have to control them. Then in Brown, you'd want to get this shithead to calm the other assholes down. This would be stupid, but it is an option.
Basically, GameFreak made all these interesting legendaries, and let them go to waste. RBY/FRLG should have had more to do with Mew/Mewtwo, and maybe the birds. I mean, Team Rocket fucking created Mewtwo, yet he's hardly mentioned. Make us have to stop him from killing Samantha or some shit. Christ.
GSC/HGSS should have incorporated the dogs and Ho-Oh and Lugia. In HG/SS, you HAVE to catch the version mascot, but why? There's no actual reason, other than that FUCKING BITCH LYRA WON'T LET YOU ADVANCE UNTIL YOU DO. And Eusine makes no sense. There's no reason for you to want Suicune, other than "HE'S A LEGENDARY". There's no GOOD reason to need to catch these idiots. If you're gonna MAKE me catch a legendary, give me a good reason. I don't mind having one out there that says "catch me if you'd like", even if that's wasting potential, but it's worse when you make me catch something and don't even say why.
Gen III was the worst for this, though. The Regis have no effect on anything, but the puzzles are SUPER-NEATO so I can let it slide. Lati@s have no effect on anything, and are just there for shits and giggles. Pokemon Adventures made them a huge part of the plot, along with the Regis and Jirachi, so why couldn't the games? But no. "HEY THIS RARE POKEMON IS FLYING AROUND GO CATCH IT" "OH OKAY" Jesus Christ.
Worst of all in Gen III was Deoxys. He's so badass-looking, and CAME FROM SPACE. AWESOME! OBVIOUSLY HE'LL BE SIGNIFICANT IN SOME WAY AND NOT BE AN EVENT POKEMON! butthurt FUCKING GAMEFREAK. In Pokemon Adventures, Team Rocket took Deoxys, and tried to use him to find Giovanni's son, Silver. Red and Mewtwo stopped him from using Deoxys, and made him his own being again. This was a good use of a legendary Pokemon. Team Rocket actually do something for once. This would make the post-game of FR/LG in the Sevii Islands much better, as it would actually have a point. Deoxys is a fucking OCEAN of untapped potential in the games, yet he's never even fucking mentioned until an event ticket you get says "COME HERE FOR NO REASON", and HE'S FUCKING ON AN ISLAND FOR NO REASON.
This isn't to say Gen IV didn't fuck up, too. The story revolves around the lake trio and the dragons, so that's six. Heatran is discussed post-game, and is part of another Galactic plot, so I'll give him a pass, too. That leaves Cresselia and Darkrai, who represent the opposite phases of the moon, Manaphy and Phione, who represent the ocean, Regigigas, who created the Regis, Shaymin, who basically represents life and nature, and Arceus, who is God.
Even fucking Rotom is unique, and was Team Galactic's scientist's best friend. You can't win him over by showing how Rotom supports you, no one has you get Rotom to show him the error of his ways. Rotom's just THERE.
The lunar duo could have some interesting conflicts, enough to make a game about. Team Luna could want to make the moon 100% dark or light, depending on the version, and you could have to stop them. In the third version, a Pokemon representing harmony (Reshiram and Zekrom!) could come in and try to stop the splintered Team Luna from doing either. Or even Shaymin could work! They could destroy the moon, which would destroy the ocean, and Shaymin could fix shit!
Manaphy and Phione suck, and could be used for post-game bullshit. Regigigas makes sense, as the other Regis were purposely retarded to find.
This leaves Arceus. God. The problem I have with Arceus is that he's God, and HE ISN'T EVEN MENTIONED BY ANYONE. Arceus could have been name-dropped for several generations, causing outcries of "WHAT IS ARCEUS", then in Generation X, they could reveal GOD. There would be one game in Gen X, Pokemon Eternal. It involves ALL THE OTHER LEGENDARIES GOING BATSHIT INSANE. To stop them, you need GOD. FUCKING GOD. You would enlist GOD's help, and calm those fuckers down. Brilliant end to the franchise, or a brilliant new beginning. It could even star Red/Green.
Of course, this is all just me flushing my brain, as I like to do. None of this will ever happen, and there'll be more awesome ideas reduced to events and random caves. What's more is most people won't be able to use these cool guys just because of how they're distributed.
I love you GameFreak, but you're all retards.
What I'm hoping for in Gen VI is a step back. Take all the Pokemon without three-stage evolution lines and look at them. Seriously look at them. For the ones who could use a new evolution to make them on-par with fully-evolved guys, or to make them an interesting choice, make them an evolution. You see all the legendaries who don't have shit to their name? Give them a reason to be there. See all the mismatched stat choices and movesets that are complete shit? Overhaul them completely. Before starting something new, fix what's broken. Fix your game engine so that double team doesn't make me want to kill myself. Get rid of all the fucking bridges. We get it, Gen V has great graphics. Don't shove them down our throats every other route. Give us a fucking dark gym. Finally explain to retards who want a light-type that fighting is the de facto light-type*. Fix everything that needs to be fixed.
*Fighting-type in Japanese is called Hero-type, and it goes along with this train of thought: Dark is the villain, who can harm the princess, but ain't got shit on the hero. Fighting is the hero, who can fuck the villain's shit up, but can't touch the princess. Psychic is the princess, who can't even touch the villain, but can destroy the hero if he tries anything stupid. This leads to interesting combinations, such as the anti-hero.