The best for me is the RPGMaker XP with Poccil Starter Kit to use, but the learnig curve is big. To master the RPG Maker XP you need some time, to master the Stater kit features you need more time, and to master RGSS you need SO much time. But you can make a ton of things easily after mastered.
DO NOT make a generic 8 Type Based GYM, a new Team and a E4 like DPP, is too overused... Make another number of GYMs or GYM based in climate, continent, Egg Group, or else!
Use the Isshu Pokémon, unless it is a Anime/Manga arc that only use regional pokémon.
If you use Fakemon, DO RIGHT. Play a game with ugly Fakemon is terrible...
Some ideas. One or another may sound madness, but we must innovate and may end up a good game. You can combine some:
-Use ONE anime arc, manga arc or movie (like the Mewtwo Strikes Back game). DO NOT try to finish a perfect anime/manga game becaus is too long for a rookie, give up in half of way is the worst thing!
-Shadow pokémon reach in a old region like Kanto! Team up with GYM Leaders and save the pokémon!
-A game were the few trainers are locked in Pre-history period! You must team up with your rival to find a way (Celebi/Dialga) to travel back in time!
-A solo pokémon game where you are one pokémon the entire game. Good for short games.
-A Kabutops (see above) who need to survive the extinction. In mid-game it is frozen and awake in the current era. Many humans (near end Team Rocket) trying to catch it while Kabutops seach for another survivors.
-You live in real world and is transported to a poké-world.
-A interplanetary game. Every planet, most have a certain type: A ice planet has ice; a hot, fire; a desert, Rock/Ground; a darkness, Dark; a special, Dragon, etc...
-You need to fight the Deoxys empire! Maybe a new boss forms?
-Dragon Ball-style game! You seach for the 7 Rayquazza pokéballs!
-A Chrono Trigger-style game! You travel around time!
-Kyogre Flood Orre and only a few areas remains like the top of Mt Battle.
-In Ruby/Sapphire the main character fail to defeat the Team Aqua/Magma and you need to save the ruined world, maybe time-travel to stop the cataclysm?
-(combine with above) The people, decided to eliminate all pokémon using super-robots! You fight in the pokémon faction. Some GYM Leaders became renegade and allied in human faction.
-A crossover versus Digimon, but the latter Digimon forms are even above Groudon/Mewtwo level!
