Isabelle and Villager share their neutral special, up special, Final Smash, dash attack, forward tilt, down tilt, up air, down air, forward air, back air, and their grabs and throws.
Their side specials, down specials, up smashes, down smashes, forward smashes, up tilts, neutral airs, and jabs are unique.
Marth and Roy share their side special, down special, down tilt, dash attack, neutral air, forward air, back air, up air, down smash, and grabs and throws.
Their neutral specials, up specials, Final Smash, up smashes, forward smashes, forward tilts, up tilts, jabs, and down airs are unique.
If we count Isabelle's up special as unique due to a slight animation difference, then the same must be done for Marth and Roy's dash attacks.
Most people would call Roy a semiclone of Marth. Why, then, would Isabelle not be called a semiclone of Villager despite the fact that they have one fewer different move from Villager than Marth and Roy do from each other? Especially when Marth and Roy's general physics and playstyles are far more different from each other than Villager and Isabelle's are.