Hi Julien,
This is an advice from Macedonian native. According to me and most of Macedonians the best city is Skopje, the capital. There is everything in the capital, the best hospitals, universities, schools... Also there is a lot of migration in Macedonia, people from other cities go to live in the capital.
Other good cities are Bitola, Stip, and Ohrid. Bitola and Stip have universities and Ohrid is a beautiful city on the shore of the Ohrid lake. There are other cities in Macedonia that are smaller like Gevgelija, Strumica, Struga, Tetovo, Prilep, Gostivar, Kratovo,Delcevo, Berovo, Negotino, Kavadarci... and all of them have their unique beauty.
If somebody needs more information can PM me.
Best Regards,
Sonja