Other situations which allow you to make multiple decisions include betrayal which could result in mini boss battles. (playstationlifestyle.net)
There are optional objective to perform if you are up to the task, and you can also find wanted posters in each level to unlock challenging mini boss fights. (gearnuke.com)
I would have these villains as mini bosses for the story to play out, before one big showdown at the end of the story. (vinylmationkingdom.com)