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The artist designers and creator Alex Hirsch thought that some characters looked better with 4 and others with 5. So it's based on design. A young Stan looked better with 4 than 5 fingers, but the older Stan looked better with 5. Hirsch said that the viewer has to think that all characers (except Ford) have 5 fingers, even when they only have 4.
Hirsch also joked sometimes before he made this statement that the people with 5 fingers had more life experience and had seen things, so that means the people with 4 fingers are more naive and innocent. That explains why Stan, Soos and Gideon have 5 and Dipper and Mabel have 4.