You can try removing the audio folder and then compress it. I guarantee that's where that size came from. However, I recommend you downgrade your music or use MIDIs, as that is a ridiculous size for something that could use an installer.
This is why while BW graphics are pretty and all, they are not ideal for an RPG Maker Game...lol.
There's no good way to compress .gif files, the reasons ROMs are so small is because they use an animation engine to animate the Pokémon with the sprites split into parts.
Like Evil Arms said, try to index the colors with Irfanview or Photoshop.
That is probably the best way to save space.
Otherwise, you'll just have to live with the big file size.
I don't really care if it's a big file size when I download a game.
One question though: Are you really going to feature all 649 Pokémon in your game?
It's REALLY hard to have all 649 Pokémon available in a game without having multiple regions.
Wouldn't it be better to make a custom Pokédex with your favorite Pokémon from all generations? That way you could lower the amount of images by 60-75%.