What flavour of quarks make up quark gluon plasma? What would it most likely cool down into, protons, neutrons, strange matter, neutronium or what?
Quark-gluon plasma is just a phase matter in QCD may enter into.
Just as a solid or a gas may be made out of any kind of atoms or molecules, quark-gluon plasma may be made out of quarks of any flavor. If you make it by heating ordinary matter, it will obviously mostly contain up- and down-quarks. It's just a phase of QCD, and it cools into whatever its constituents can cool into.
The quark model has developed to fit a great number of measurements
In particle physics, the quark model is a classification scheme for hadrons in terms of their valence quarks—the quarks and antiquarks which give rise to the quantum numbers of the hadrons. The quark model underlies "flavor SU(3)", or the Eightfold Way, the successful classification scheme organizing the large number of lighter hadrons
Hadrons are not really "elementary", and can be regarded as bound states of their "valence quarks" and antiquarks, which give rise to the quantum numbers of the hadrons. These quantum numbers are labels identifying the hadrons, and are of two kinds. One set comes from the Poincaré symmetry—JPC, where J, P and C stand for the total angular momentum, P-symmetry, and C-symmetry, respectively.
The remaining are flavour quantum numbers such as the isospin, strangeness, charm, and so on. The strong interactions binding the quarks together are insensitive to these quantum numbers, so variation of them leads to systematic mass and coupling relationships among the hadrons in the same flavor multiplet.
Looking at the eightfold way of calassifying into flavor SU(3) the measured resonances/particles we note that one of the axis in the plot is proportional to the mass of the resonances.
baryon decuplet -------------------------------- meson octet
The strangeness equal zero state has the lowest masses in both. The quark gluon plasma happens at very high energies, proposed in the hypothesis for the evolution from the singularity of the Big Bang as the energy falls due to the expansion of the universe. As the plasma cools there will be all flavors according to the available energy to generate the masses , further cooling will disfavor the hadrons with strange quantum numbers, which will follow the normal decay paths, until protons and neutrons can form and the plasma stops existing, at about a microsecond from the Big Bang.
The other way, trying to create a quark gluon plasma is being studied at the LHC at the moment .
So the quark gluon plasma does not have a unique flavor but is a statistical distribution of flavors, depending on the energy available and the quark model.
There are two conserved charges, baryon number and electric charge. This means that the total baryon number and charge of a quark gluon plasma are determined by how it was made. Everything else is determined by thermal equilibrium (if there is enough time), and kinetics (if there is not enough time to fully equilibrate).
In a heavy ion collision there is not enough time for weak interactions to equilibrate, so net flavor (up minus anti-up, down minus anti-down, strange minus anti-stange, charm minus anti-charm, .. ) is effectively conserved as well. In the quark core of a neutron star (if such a thing exists) weak equilibrium is reached.
In a relativistic heavy ion collision, as a first approximation, you can think of all quarks as heaving been pair-produced by gluons. This means that the QGP has no net flavor or baryon number. Of course, the initial nuclei had net baryon number and a slight excess of neutrons over protons (i.e. down over up). Most of this goes down the beam pipe, but some of it ends up in the plasma, so there is a slight excess of quarks over anti-quarks, and a slight excess of down over up.
If you look at the total number (up plus anti-up, down plus anti-down, ..) rather than the net number (up minus anti-up, ..), then in thermal equilibrium there will be a tiny excess of up over down, and a larger excess of up over strange, because of the mass ordering of the quarks.