Okay, I'm putting together some of the characters that are portrayed very different from canon (taken from my knowledge, Touhou Wiki, and what I read here), not to mention the differences between both interpretations.
Meiling
Canon: Average, competent, gets respect, takes afternoon siestas
Fanon: Incompetent, likes to sleep, Sakuya's punching bag
Tenshi
Canon: Dislikes boredom, loves to fight, spoiled
Fanon: Loves to get beaten up
Kaguya
Canon: Ditzy, anxious to do various things, cheerful, gets worked up when doing something she wants to do
Fanon: Lazy, NEET, obsessed with video games and the Internet
Komachi
Canon: Serious with work
Fanon: Snorlax
Letty
Canon: Doesn't care about Cirno and doesn't even want to be compared to her
Fanon: Motherly relationship towards her
Alice
Canon: Calm, collected, kind, looks and acts cold, not the conversation type
Fanon: Tsundere
Koakuma
Canon: Mischievous
Fanon: Patchouli's obedient servant (it might be the same case in canon)
Yuyuko
Canon: Easy-going, smart, full of wisdom and insight, whimsical
Fanon: Snorlax (minus the sleeping part), Mystia's worst nightmare
Yuuka
Canon: Likes to tease and mess with people
Fanon: Ultimate Sadistic Creature
Koishi
Canon: Cheerful, curious, hyperactive (I think...)
Fanon: Psycho