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I think its better the way she's done in FRLG. She doesn't need to be another character. Anything you write her doing would then have to be swapped for Red if someone chose the female character. I could see her getting the starter weak to yours (but strong against Blue)
Some general ideas of where she could appear:
Viridian - Oh Red, here's how to catch Pokemon
Route 22 - Oh Red, you can't go to the Elite Four without badges (replace the Blue encounter)
Pewter - Red, you need to defeat Gym leaders to become stronger and beat Blue. Maybe he will stop acting weird if you beat him.
Mt Moon - Some scary people are up ahead. Please help me get rid of them
Vermilion - Wow that's a big ship.
Dark Cave entrance - I want to see how I've grown
Lavender - I think I saw Blue go into that building. Red your Pokemon are tired after a long journey. Let me heal them/go to the PMC
Fuschia - I got lost in the Safari Zone, but now we can battle
Route 12-15 - I love the ocean. Let's battle
Route 22 - Blue already went ahead. Let's battle.
Random champion (she does have the advantage over Blue)
