One of the things that's really cool about 7th Sea 2nd Edition is the way it handles its villains. Mechanically a villain is effectively one stat, and then has whatever abilities you want them to have. Why? Because villains are exclusively the domain of the GM, and since the rules tend to not apply to the GM - who can make and change them as they please - why bog it down with extra mechanics?
Some people may balk, but this is no different than making a custom monster in D&D or pathfinder, or building an encounter in any system. Yes, there are guidelines, but if you - as the GM - want brand new PCs to fight an epic level monster nothing is stopping you. It may not be fun for your group, but that is between you and them, not the rule system.
However, what I really like about the Villain system is how it lets you engage with the villain as a player in a meaningful way that impacts the game. To explain that, we need to explain how villains work.
The Villain Strength Stat
A villain in 7th Sea 2nd Edition is one stat: Villain Strength. Villain Strength determines the number of dice that the villain rolls in any check to determine how many raises they get to use that round of action. However, Villain Strength is actually broken down into two sub stats: The Villain Themselves - i.e. how dangerous the villain is just on their own, and the Villain's Influence.
There is a mini-game for the GM with villains where the villain wagers influence on plans, where the success or failure of the plan determines whether the villain gains or loses influence.
There are also things a villain can 'spend' or 'invest' their influence into - including hiring other villains, henchmen, escape plans, etc if you want to get into it. This way your Big Bad can gain power without having to reveal themselves to the hero, and your heroes can work their way up to the big bad.
The Rise and Fall of a Villain
What I like about this system is it gives way for a villain to have a full arc with the PCs depending on how things play out. It is possible to have a villain succeed at plans, gain influence - and thus become more prominent and dangerous - and then lose influence as things go against them. You get a full arc for the villain.
The system being built to handle this is also really neat. There is a meaningful way to track and measure the success of the villains plans. This in turn encourages you to set plans in a meaningful way - and to plan them how the villain would. Combine this with your GM brain, and you are naturally encouraged to set up Xanatos Gambits for your villain, enabling scenarios where the PCs can have a victory, but the villain still gets what they want out of it.
From Overwhelming to Manageable
My favorite part of this mechanic is that it encourages - and allows - you to build up to facing the villain. A villain can be outright overwhelming for the PCs in a straight up fight with their full influence. Rolling enough dice to have more raises than several PCs combined. Not the thing you want to go up against.
However, by working up to the problem, your heroes can foil the villains plans, take out their base of support, and whittle the hero down to make them more manageable in a fight.
This is something you can do in any game - where the villain has all their hench people and back up plans and clone stashes and whatever which the PCs take out - but the system covering for that bakes it in naturally and helps make you a better GM by encompassing these things while also giving the PCs a meaningful way to track their progress, or see the benefits of what they've done.
It can be a great feeling to see that the villain now only gets half as many dice to roll against you in combat, because you've spent the last couple sessions knocking out their pillars of support.