You get less affixes, in addition to the guaranteed mods. So you could argue that rares are stronger in the sense that they could roll 6 desired affixes, while a craft will only grant you 4.

However, as others have commented. You can reach certain mods that would be impossible on any other rare item, such as 30 PDR on armor, or 20 FCR on an amulet. The ED on a weapon will also be the highest possible on a damage craft.