The 3.5 drives even at the same rpm would tend to perform a bit better. The magnetic head reads data from the outside of the platter(s) to the center typically. In that case, the outer portion of the platter is rotating faster. The rpm is the spindle speed at the center. As the platter gets larger the speed ratio increases at the outer edge and the more data that can be read before the head has to move inward to the increasingly smaller and smaller 'rings' or 'spirals'.
Sort of like ssd's, larger capacity ssd's are not only capable of holding more data they actually tend to perform better. The above consideration for mechanical drives of course depends on everything else being equal, actual drive properties, specialty methods...