Swords are the real world ubiquitous, full sized weapon. While the spear and its big brother the polearm dominate on the battlefield and in places where someone is standing guard, swords are the weapons that nobles and mercenaries alike (depending on local laws) will simply have on them at almost all times. They may feel overused in fiction, but this is a reflection of reality.
Also, note that I said full-sized weapons. Daggers, of course, were everywhere. But daggers were also necessary tools of life, and all other things being equal, a man with a sword beats a man with a dagger, even if the man with the dagger would generally be considered the better fighter.
Staffs have their place too of course, but usually as an option for someone who is traveling. Have to deal with a staff all the time is about as bad as having to deal with a spear; if you are not going to use a staff as the tool it is, you are probably not carrying it around in case you need to use it as a weapon.
That said, once magic enters the field, you may have more options. If you world includes the ability to store and summon a weapon with barely a thought, you can potentially summon the most useful weapon for the circumstance, assuming you have one stored. A polearm in a crowded area with lots of non-combatants nearby is a bad idea, but a fast blade like a rapier is a good choice, along with a parrying dagger or shield, depending on other circumstances.
And of course, at sufficient range, one should be using a bow. Remember, a bow was a samurai's *first* weapon in a battle. Their blade was only drawn once the enemy was too close. And they fired from horseback with specialized longbows that were fired from the bottom third.
Flails and maces do have their place on the battlefield, but mostly for use against metal armor and such. Against flesh and cloth, you want a sharp blade. So what type of fight are they in? Are they fighting monsters? Spears/polearms when you have the room, swords when you don't, unless they have thick hide, in which case you might want an axe, or if they have large, hard scales, you might want a mace or a flail.
Team work is also good here. I have a fight sequence where one person plants the butt of his polearm against the monster charging them, and once it is impaled, struggles to hold it in place long enough for another person to wail on it's head with falcatas. While they are swords, the distribution of their weight and mass gives them some of the same impact as an axe or a mace.
So, the favored weapon of your protagonist should entirely depend upon the 1) circumstances of their life, 2) the circumstances of the fight, and 3) the consequences of how magic interacts with weapons and weapon choices in your world. If your punch can hit someone with a fist of air from 30' away, you are not as worried about whether or not you have a sword.
