I like the idea of a rarity leaderboard, but the way it's described sound still way too much abusable IMHO.
There is games like Magicka 2 which are full of ultra rare trophies while not being really hard, and on the other hand there is really hard or long games to complete just because of one single trophy.
It would be more fair i think to give points for the rarest trophy obtained in a game, weighted by the completion of the game :
For exemple :
My rarest trophy in a game have a 4% rarity, and 4% worth 4000 points. I have 80% completion on that game, so i will earn 80% of 4000 points.
This way, it still negates the points gain of skipped visual novel, (0% or 100% of 0 points is still 0) while preventing over rewarding games for no reason.