How to fix: The number of properties in the Dependent and Principal Roles in a relationship constraint must be identical?

The reason for the error are incorrectly configured relations in your model. This is not correct:

    one.HasRequired(t => t.Two)
        .WithMany(s => s.Ones)
        .HasForeignKey(t => t.TwoId);

    one.HasRequired(t => t.Three)
        .WithMany(s => s.Ones)
        .HasForeignKey(t => t.ThreeId);

It should be:

    one.HasRequired(t => t.Two)
        .WithMany(s => s.Ones)
        .HasForeignKey(t => new { t.TwoId, t.ThreeId });

Because dependent’s FK must contain all columns of principal PK. You must also remove navigation property from Three to One.