I worked a long time on creating a limitation system with this and I'm still not sure I'm happy with what I came up with.
Basically, you can take a limitation and if you get limited by it in a meaningful way; miss an opportunity, fail, get injured, etc, you get an Action Point, But Better, which isn't limited by the number per turn you can burn.
So if you're addicted to something and you don't get your fix and start taking penalties. You get a point whenever those penalties accrue.
Or if you've got an arch enemy, you get the point whenever that enemy pops up.