I do feel differently from you on this Hearth Cricket. I activate my jewelery and use it for healing (etc.) purposes just as I do my raw crystals. I even include the silver or gold metal as they both have metaphysical properties as well.
There most assuredly is a difference in the type of energy you get, however, I do not think one is better or worse than the other.
Generally, I've noticed that cut stones have a sharper, more piercing energy, while tumbled stones or cabochons (the smoothly rounded ovals) have a softer, gentled energy. Raw crystals/gemstones are in a more natural state. It is good to take this into account when choosing a stone for a certain purpose.
The great thing about activating one's jewelery is that it can be so inconspicuous and so powerful at the same time.
Okay, so I just thought of something that might make a difference in your choice of cut gemstones versus crystals in their natural state. A cut stone, in jewelery, is more likely to have been mined and processed for the specific purpose of being a piece of jewelery, while a natural mineral is more likely to have been mined and processed with the specific purpose of being appreciated for it's inherent qualities (as a mineralogical specimen or as a metaphysical tool). If you believe that crystals pick up on the energies around them, you might want one that had less of that processing into a piece of pretty bling bling.