Generally it is said that current is due to the flow of electrons; how can we make this claim? I mean, generally we say the atom contains a nucleus which consists protons (positively charged particles), neutrons and, in the outer orbitals, electrons (negatively charged particles). What my question is, how can they generalize that an atom nucleus consists of protons and orbitals contain electrons, could it be the reverse?
From classical models, the electron and a proton revolve around their mutual center of mass, which approximately lies on the proton itself, because the proton has a significantly higher mass than the electron. This is why electrons revolve "around" the proton, and hence form the outer layer of an atom.
Quantum mechanically, electrons could never form a nucleus because of their similar charge repulsion. Protons can form nuclei because protons are made up of quarks, and these quarks can bind protons and neutrons together via the strong force, which (as the name suggests) is quite stronger than the electromagnetic force. This is why electrons occupy orbitals and protons and neutrons form the nucleus. Electrons, also, because of their extremely light mass, cannot stay as 'localized' as a proton or neutron can.
Everything we know about nuclei is described by Quantum Mechanics. We'd know we were wrong if we started it out from a wrong assumption. (e.g. like the one you suggested at the end of your question)
If I understand your questions correctly: Yes, it can be somehow the other way around.
But we do "know": There are two sort of particles in here, one of them has a certain charge and is light, the other has the opposite charge and is heavy. You can then claim that the heavy ones rather stay in place and the light ones sprint around and make up the current.
The names (proton/electron) and, as far as I know, the sign of the charge (only the sign of $q_1*q_2$ is important) are arbitrary. This means it can't stay close to the center while the heavy one is flying around.
Edit: If you think about the light one staying in the middle: In the center-of-momentum frame, the momenta $p_i=m_i*v_I$ (classical physics) have the same size. So the light one has to be faster (factor $2000$).
Generally it is said that current is due to the flow of electrons; how can we make this claim?
If the wire is in a magnetic field the moving charges will move in a circle based on the magnetic force. This happens until enough charge imbalance develops on the edges of the wire to produce an equal and opposite electric force. But measuring the voltage difference across the edges (called the Hall voltage) and comparing it to the magnetic field can find out the sign of the moving charges.
Which is sometimes positive and sometimes negative, for instance if you have ionic fluids there might be moving ions of either charge sign.
I mean, generally we say the atom contains a nucleus which consists protons (positively charged particles), neutrons and, in the outer orbitals, electrons (negatively charged particles). What my question is, how can they generalize that an atom nucleus consists of protons and orbitals contain electrons, could it be the reverse?
The nucleons have strong attractive forces that can hold them together dispute the fact that they electrically repel each other. So they can have a big charge to attract many electrons.
Electrons do not have any forces to attract each other. So they can't attract a bunch of protons. And if it is just one electron and one proton then it's just hydrogen.
And even in that case the electrical interaction between the two is just as strong by the proton is 2000 times as heavy so it simply doesn't move as much. So even then the electrons can be more spread out.
We don't expect these things to change, the proton is always 2000 times as massive and it always has a strong attractive force to other protons that are about a femtometer away but the electron does not. So we don't expect this to change.
But the real reason the electrons move is that the different nucleuses can space themselves out regularly while the electron form a joint kind of pattern that acts together like a fairly solid object with some electrons left over free to move, the more that are free to move the better a conductor the solid is. And that's why in a good conductor it is electrons that are moving.
The Hall effect (that voltage on the edges) is merely how we confirm this is what is happening, it isn't why it is happening.