I am brainstorming the options that only villains would have. Here's what I have so far...
Tenacity. I included this in my play test earlier this week and loved it. A villain gets opportunities to negate successful actions by heroes against them, by attempting a Feat. This is totally the Terminator.
Henchmen. You have a group of mooks that will take attacks for you. You attempt a CHA check, and if successful a mook is there to pull in front of the energy blast or throw on the grenade (quite literally). Joker, Penguin...
Controlled Chaos. You have a wild die to roll once per round; it can either go really well (exploding for extra dice if you roll max) or really bad (things go bottom up on a 1). Joker and Harley have this.
Weaponsmith. You have a new super weapon every time you appear; this could be a mech (I mean, it's probably a mech), a single-use battle suit, an experimental walker (which is kinda like a mech, if we're being honest)... a tank. You get to build this thing and it is at your level. There would have to be examples of how to apply this, although the GM should have a LOT of leeway here. This is Luthor thing.
Escape Plan. You always have your exit plan in place. Any time the battle turns, you can attempt a Feat to beat a hasty retreat. I don't love this one mechanically (because it doesn't make sense that the villain is suddenly gone), but it happens in comics... too much. I don't know how much I like this. It is source material, but it's also going to make players really, really mad. Every time they are about to beat the villain, he uses an action, attempts a Feat, and is GONE.
Just these five cover a lot of ground, and give variety. Before, the idea that villains might show up with a battle walker was kind of (okay, completely) hand waved. Now, there'd be a very loose (but clear) set of expectations for how to build a device for a weaponsmith. I did some reading around archetypes, and I don't know that I want to structure archetypes specifically; villains would also have origins and a purpose statement, so these are enough to frame out the villain. Going with more concrete and structured archetypes for villains doesn't align with the freeform approach to hero building that is already in place. I definitely want a few more mechanical options for villains, but this is a decent starter list.