Some high-energy experiments (RHIC, LHC) use ion-ion collisions instead of proton-proton collisions. Although the total center-of-mass energy is indeed higher than p-p collisions, it might happen that the total energy per nucleon is actually lower. What are the advantages of using ion-ion collisions (e.g. gold-gold or lead-lead) instead of proton-proton collisions, considering the same accelerator?
As a clarification the energy per nucleon is always lower: for example, currently in the LHC the proton top energy is 3.5 TeV. Now the Pb energy is 3.5 TeV times Z so the energy per nucleon is 3.5*Z/A and A is greater than Z for every nucleus (except the proton where it is equal to one).
But the goal of ion-ion collision is not to increase the total energy or the energy per nucleon: it is to obtain a different type of collision.
It should be noted than in a proton-proton collision, the energy involved in the real collision process is variable: each quark and gluon carry a fraction of the energy of the proton, and hard collision involve a collision between a quark/gluon of one proton against a quark/gluon of the other.
In the case of ion-ion collision you have the same process: the energy is shared by the protons/neutrons and they can have different energies.
The goal of such collision is also to obtain a volume (bigger than in a p-p collision) with a very high energy density. In such a volume, a "state of matter" called quark-gluon-plasma is believed to be possibly created. The study of this QGP is one of the main goal of the ALICE experiment at the LHC.
A few references: