If I had any coding skills, I would actually make the games floating around in my head. Pokemon/Sailor Moon crossovers. Real original, right?
But they would be different from the main Pokemon games.
In the games (the original and the sequel or sequels), you play as Chibi-Usa/Rini. (It would be Rini, because these would be English games, but I think of the characters with their Japanese names.
) Your Pokemon start at level 5 and are locked to your party. In the original, because you've traveled back in time, just like Spiky-Eared Pichu they can't evolve. However, they also can't gain experience or happiness. Your job is to go back in time and help Ami/Amy, Rei/Raye, Makoto/Lita, Minako/Mina, and of course Usagi/Serena to fix the timeline by defeating members of the Black Moon Clan. Two-on-one battling has your useless Pokemon (all of them Normal-type, and 5/6 baby Pokemon) helping one of your current partner's Pokemon to defeat a single opponent. Almost all your moves are status moves, and (again, explained away by time travel) your Pokemon can't learn TMs or HMs (and there is no move tutor). The opposite is true for the few battles fought in the future: your friends' Pokemon can't gain experience or happiness, or learn new moves or evolve (although yours can). So you'd better get them leveled up before they travel to the future for the final few battles!
As well as grunts (here called drones), the Ayakashi Sisters and Rubeus are battled in the past. Esmeraude, Sapphire, Dimande, and Wiseman are all fought in the future... as well as Black Lady! Black Lady is YOU, from an alternate future in which the Black Moon Clan has won. Setsuna/Trista shows up and tries to beat her, but fails. So before defeating Wiseman, you must first help Usagi/Serena defeat yourself.
The past contains Pokemon Centers/PokeMarts where you can get free healing, and in the future you can heal your party(s) by visiting the trapped future Usagi/Serena in the Crystal Palace. Mamoru/Darien's only battle is against Rubeus. Future Mamoru/Darien occasionally appears around the Crystal Palace to give advice. Everyone is in civilian clothes, as the Senshi don't exist in this universe. When you are battling with a partner, his/her Pokemon's attacks are chosen at random from the four it knows. A two-on-one battle ends either when your partner's Pokemon faints or your opponent's does. You may switch your own Pokemon out during battle, if you so choose. All games in both series employ several event/custom sprite Pokemon from PokeFarm and novelty Pokemon from GPX+.
The game starts in the future with an attack on the Crystal Palace, where the Champion and Elite Four await challengers. Setsuna/Trista talks to you, the screen goes black, and you find yourself at Ilex Shrine. She gives you a Rainbow Wing and Silver Wing (no use in-game) and tells you to "go back and make things right". Celebi appears, and the player whites out. You wake up in a house surrounded by curious strangers: Ikuko-Mama, Kenji-Papa, Usagi/Serena, Shingo/Sammy, and Mamoru/Darien. Usagi/Serena and Mamoru/Darien take you aside and speak to you.
The sequel involves going back in time again, this time with the base forms of the Pokemon you started with (ie, Jigglypuff instead of Igglybuff), to help defeat the Dead Moon Circus. You get a Clear Bell, which does summon Suicune, although he acts as a partner Pokemon in a single two-on-one battle rather than as a wild Pokemon to be caught. The Clear Bell can be used in any location, but only works once, so save it for one of the final few battles, if you can. Michiru/Michelle also has an AuroraTicket, which will let you get to Full Moon Island, encounter Cresselia, and find the Lunar Wing. If you are in possession of the Lunar Wing during the final boss battle, Cresselia will be your partner Pokemon against Nehellenia/Nephrenia's Darkrai.
The other version of these games takes place entirely in the future. Your party is made up of the same level 5 Normal-types as the first game (Happiny, Togepi, etc.) but now they can evolve and accrue happiness and experience. They can also learn TMs and HMs (although HMs aren't needed to get anywhere or complete the storyline), as well as learning moves through the normal level-up method. There are eight gym leaders, the Elite Four, and a Champion to defeat. The gym leaders and their specialties are, in order: Jadeite/Jedite (rock), Nephrite/Nephlite (ghost), Zoisite/Zoycite (ground), Kunzite/Malachite (dark), Mamoru (fighting), Haruka/Amara (flying), Michiru/Michelle (water), and Setsuna/Trista (time and space). No, "time and space" isn't a new type, it just represents the Pokemon she chooses to specialize in. Zoisite/Zoycite is male in these versions, as in the manga. You don't have a rival, but your shy, sickly friend Hotaru occasionally battles you with her Absol for fun/training. Over the course of the game, you help her become more self-confident and outgoing.
The Elite Four and their types, in order, are: Ami/Amy (ice), Rei/Raye (fire), Makoto/Lita (electric), and Minako/Mina (love). Again, love isn't its own type, that's just the theme she uses. The Champion is, of course, Usagi/Serena, who specializes in Normal-type Pokemon. Since your Pokemon are locked to your party (you may battle wild Pokemon but not catch them), you should end up with almost exactly the same party as she does, with one difference: her Lopunny is the Sunnie (Lopunny) from PokeFarm, while yours starts as a normal--but shiny--Buneary which should eventually evolve into a normal-but-shiny Lopunny.
If you beat your mother, you become Champion of the region. Huzzah!
Also you have to beat Shadow Galactica along the way.
The sequel is that Chibi-Usa/Rini has become Champion of the region. Haruka/Amara, Michiru/Michelle and Setsuna/Trista are still the last three gym leaders. Helios is the fifth gym leader. The Elite Four are Vesta (normal), Juno (fighting), Pallas (don't know yet) and Ceres (flowers). The Champion is an older Chibi-Usa/Rini. I'm... still working on who the first four gym leaders are (fourth will probably be Hotaru) and who the baddies might be. In this, you're a normal player character who can catch, evolve, switch out, etc. as normal. Neither of the games in these two series allows you to catch Legendary Pokemon, although the final boss in the first game has a Legendary in her service.
Well, that was a huge wall of text. Presumably none of you actually read any of it, but hey--it's good to get ideas down.