One thing I was thinking of is a special Death Move for villains called "No One Could Survive That" that basically compels the players to not chase down a villain. Maybe everyone gets an extra Hope at the start of the next session?
The trouble with that is it's a bit "I'll gladly pay you Tuesday for a hamburger today", which is to say, you're essentially giving the players a cheap IOU for something you should be paying for in your own money. I would suggest paying Fear is going to be less insulting and better accepted (probably relative to the scale of the villain too, I think if you try and get away with 1 Fear that's going to kind of feel rubbish, 2-3 would be more like). Having to pay Fear also means you can't just blast through all your Fear in an encounter and get away anyway, you have to hold back a bit and have the villain escape legit.
Also I'd suggest the Death Move maybe means the villain can't be directly involved in like, the next 3 sessions or something.
I think I might have the following requirements to the move:
1) 1-3 Fear contingent on the importance of the villain (i.e. named mooks 1, notable bruisers and sidekicks 2, actual masterminds and monsters 3).
2) Villain can't directly (i.e. in combat or social) fight the PCs for 1d3 sessions (or just 3). He has to run away again (probably only costing 1 Fear this time) if they track him down (masterminds can still mastermind but should take care not to get caught - make sure your base has an emergency exit, preferably involving some kind of rocket or train or a rocket-propelled train-sled!).
Alternative 2) The villain can't use this move again until they have been captured/defeated/imprisoned. So the next time they meet the PCs, they're going down, or escaping "legit" (i.e. running away early in the fight etc.).
3) Villain has to have at least 1 Stress or HP box left unchecked when he pulls this move.
I do think the basic framework for Daggerheart, with different classes, and Powers instead of Weapons/Armour/Domains could make for a particularly good supers RPG. I am not the man to write it though!