Like the plot of b/w is to [major spoilers]

Or in Platinum

Oh well I do have a plot that I was working on one day when I was board. They fight team NeoGen. The villans

But everything else isn't done

hrmm, guess the best thing to do now would be to just think up original concepts for pokemon.

The Starter Pokemon will come first

Staying with the standard grass/fire/water?

Yes

For the Water starter, how about a dolphin Pokemon? Possibly Water/Psychic in later stages(since Dolphins are known to be very intelligent) and specially based. For the Fire starter, how about a Volcano Rabbit Pokemon? There are rabbit Pokemon already though, so a different idea might be better. For the Grass starter, maybe a mistletoe Pokemon? It is commonly associated with kissing and Christmas and other happy things like that, while it's actually a weed that takes nutrition from other plants, so Grass/Dark typing is an option.

Any other thoughts/ideas?

pretty good romeert we can have a start now.

Grass-we could defiantly make it a type of plant or so like hoppip or
vileplume.

Fire-Volcanic rabbit great idea.

Water-I think baby shark would be a better and easier in my opinion

For the Team Maybe we should put Team Rocket (Corporation) as a rival group.
The leader can be the champion and after you defeat him they continue with exec and the team divides into there own faction.