Features
Geographically, I want a tundra. There's been ice caves and snowy paths, but no tundras. 'Bout time we need a tundra. And a savanna and a rainforest- maybe for a Safari Zone Pokemon Reserve. I could imagine a portion of the plot to be on defending a Pokemon Reserve from an evil team (one that would cut off tails of Slowpokes).
I think gaming is advanced enough to allow the customization of your trainer. For example, when beginning your game, instead of getting that lengthy speech of the Pokemon world and how exciting and mysterious it is from the Pokemon professor, you are handed a forum at a Pokemon Center to fill out in order to obtain a Pokemon Training Licenses that would include various information such as your name, birthdate, skin tone, hair colour, eye colour, gender, and age. While the trainer sprite will be dressed in simple clothes at the beginning, you could always go out and buy clothes in Department stores.
I'd like to see a few changes (maybe quite a few) in Pokemon types. Not only should there be the addition of at most three types (Light, Sound, and ???), there should be some changes in the physics of types. For a few examples, poison needs to be super-effective against fighting type. I've thought that poison was super effective against fighting types when I played Pokemon Stadium, but it really sucks to have poison only super-effective against a type that already has so many other weaknesses. There should be some elemental type changes in some Pokemon in my opinion, such as:
Charizard- Fire/Dragon
Blastoise- Water/Steel (it has metal cannons coming out of its shell for Arceus's sake!)
Ninetails- Fire/Ghost (who could not forget that anime episode!?!)
Arcanine- Fire/Light
Gyarados- Water/Dragon
Meganium- Grass/Light
Typhlosion- Fire/Ground
Feraligatr- Water/Dark (or Fighting)
Noctowl- Psychic/Flying
Ampharos- Electric/Fighting
Celebi- Bug/Psychic (finally, a legendary Bug Pokemon)
Sceptile- Grass/Dragon
Gardevoir- Psychic/Ghost
Milotic- Water/Dragon
Glalie- Ice/Dark
Empoleon- Water/Ice (it's a penguin...)
Luxray- Electric/Dark
Most Normal/Flying types -> Flying type
I'd like to see seasons come into play into the game. The game could have an in-game calendar that bases the seasons on the moon of the month. Therefore, one month will usually be one complete cycle (and then some) of seasons. Seasons, like the night and day feature, may also determine what Pokemon are available (migrating Pokemon should be implemented) and may have other bonus effects such as well.
Pokemon
Starters
I thought it would be neat if the three starters began as Dark, Psychic, and Fighting (or Light), and later gained the Grass, Fire, and Water types respectively (for example, the Psychic type may learn Will-o-Wisp before it levels up enough to evolve and gain fire as a second type). I was thinking the Dark starter should start as a fawn, evolve into an elk, then become a moose with vines through its rack. The Psychic starter should start out as a lion cub, then a lion undergoing maturity, then a lion with a mane of flame. The fighting or light type may start as a bipedal narwhal-thing (but still good on the eyes) and evolve to have a much longer tooth. Note how all three interpretations of starters have an outstanding trait showing masculinity. Only males and special females (females given as starters) may possess those traits which enable them to perform a strong move with that trait.
Here's some other Pokemon types I'd like to see:
Bug/Fire
Grass/Fire (Burning Bush Pokemon)
Seasonal Birds (Hummingbird, Swan, Turkey, and Geese)
Falcon/Eagle
Platypus (Females Water, Males Water/Poison)
Fire/Water (Steam Pokemon)
Fighting/Flying (Superhero)
Psychic/Dark (Supervillan)
Dragon/Bug
Ground/Dark
Cooking/Gourmet Pokemon
Muskrat Pokemon
Ghost/Grass Legendary
Ghost/Fire Legendary
Ghost/Water Legendary (These three would make a trio and may be inspired by that one anime episode when Brock and James fall in love with a ghost)
Rock/Fighting, Rock/Psychic, Rock/Dragon Mascot Trio (Maybe a Past, Present, and Future Theme featuring Dialga)