Are the hero creation rules strictly for players, or do you create certain NPCs like other heroes with those?
If you're playing a "villain" campaign, do the players create their villains using the hero rules, or the villain rules? If the answer here is that the villainous PCs are created using the hero rules, then are the hero NPCs created using the villain rules?
The PCs encounter dastardly, "Mirror Universe" versions of themselves. That's a common trope, yeah? Are these villains created using the hero rules (essentially just (usually) carbon copies of the PCs), or do you, the GM, try to recreate the heroes using the very different villain creation rules?
Just to confirm... whether you are creating SHIELD agents, or Hydra agents, you still simply use the minion and lieutenant creation rules, correct?
I'd say if a player is going to use a character then hero creation rules. Otherwise I'd use minions, lieutenant, and villain rules for creating other NPCs. If you're making mirror versions of heroes I'd just say if there's an ability you know they use a lot I'd say make your own twisted version of it.
I'd reccomend using the Villain rules for "evil twins", even if it means you have to tweak and/or houserule them a bit to get what you want.
For one thing, players will expect their moustached evil versions to not be carbon copies - any mechanical differences can and will be easily chalked up to the alternate universe effect (or whatever equivalent you've got going based on how their evil twins are fighting them).
For another, as a GM the very thought of actually trying to run H different full-fledged characters exhausts me! One of the things that Villains do very well is that they are much easier to run than a hero character, while still *feeling* on par with them.
As far as a "Villain PC" campaign, they should use the hero creation rules, for much the same reason - the very streamlining that makes NPC villains manageable for a GM will cause a player who isn't juggling all the other things become bored to tears!
It depends. You could make an NPC ally as a full hero, but you could also just make them as an Lt.
There is also nothing stopping you from making an antaganist using the hero creation rules. It would lead to a different fight dynamic. Villains by and large come in all guns abalzing with all of their abilities unlocked, while a fight with an enemy created as a hero would unlocked more as the fight went on. Which is a thing i would like to see in future books for villain creation. A hero is usually going to be weaker then a villain, though you can go out of your way to make a villain weaker with some of the options.
If you wanted to go mirror universe evil twins using the hero creation rules to fight your party, what I would do is not copy them exactly but switch either their archtype or power source to make them a little bit different.
For a hero NPC, you can also just have them be an effect. Urban Infestation has examples of this. This could be something like "On their turn, removes one d8 or smaller villain minion" or "On their turn, boosts a hero with a d8". This allows the story to focus on the players and puts the NPC into the background.
This conversation is one of the things I really like about these rules. In Champions, I'll use or re-skin an existing character as a villain, but I'll rarely make my own as GM because it takes too much time. This system allows me to make interesting villains with just a few steps.
The Lieutenant rules allow me to use Jobber villains. For every enemy agent, I don't have to worry about any original stats.
For an NPC Ally, I'd likely simplify them to an "effect" in the scene as Rabit mentions. In this system, I think such a shortcut is not only easier, but feels like it fits the system as a whole. I could do the same thing in Champions, but it would feel off.
Late to the party, but if the allied NPC is going to have a major impact on the fight (which works sometimes for story reasons, but isn't something you probably want to do all the time), it can be fun to give them a full PC sheet. Just remember to count them as an extra hero when designing encounters!
Villains, Leiutenants, and Minions are really designed as resisting forces for heroes. They are not designed with "villainy" in mind so much as they are designed to be challenges for PCs. Even if my group had to fight Legacy (but it's all a big misunderstanding - you know the trope), I'd write him up using the Villain rules.
And because of that, I would always create PCs using the Hero creation rules, whether they were immoral jerks or middle-of-the-road anti-heroes. "Hero" is more the expected personality of your PCs than it is a prescription for how they must behave.
Similarly, foes of any variety - villains, monsters, misunderstood aliens, Inverse-verse heroes, or a malfunctioning Benchmark - I'd use the Villains/Lieutenants/Minions rules.
And, as pointed out above, there's lots of ways to let NPCs help the players without a full character sheet - you could just represent them by using one of the Out abilities or something. This wouldn't be too imbalancing for the most part, but you'd want to be careful.