I was reading the TV Tropes entry for Madden into Misanthropy, which mentioned that Legacy of Kain: Blood Omen had a pedophilic doll-maker as a character, which suddenly catapulted my brain into a review I read about a video game RPG, I think a JRPG, which had a party member whose abilities were based on the dolls he crafted, I think with a mechanic where one of the ways to improve him was to either find new dolls for him (and I'm pretty sure it was a him), or materials for him to craft them. I believe I would have read this as a magazine review somewhere in the mid-1990s, but my memories are very hazy. If I recall correctly, the review commented that all of the characters in the RPG were a bit mechanically unusual, with this being part of the draw to the game. I don't remember what system it said the game was on, although part of me wants to think this was an SNES or Megadrive game, maybe as new as the Sony Playstation.
I'm not 100%, but casting through my memory of the time, I remembered reading a review of one of the Shadow Hearts games, and thinking I wanted to check it out some day. Searching for
Shadow Hearts dollmaker led me to Shadow Hearts: Covenant and Gepetto, who only has one doll which he uses for his attacks, Cornelia, which he can buy dresses for to change her elemental affinities and add abilities.
Not much is known about Gepetto's life. It is generally known that he was a famous puppeteer in the theaters of Paris. He is still relatively well-known but his popularity has faded. He had a young daughter named Cornelia. The puppet he uses for battle is an exact replica of her. Also, he is the brother-in-law of Father Morris Elliot and the uncle of Alice Elliot. When he was younger, his daughter died at an early age. By the beginning of the game, his wife has died and he is living with Yuri.
It's later hardware than I thought, the PS2.