Deus Ex Human Revolution's initial release was the worst about this. A bunch of people who took the skills and inventory for non-lethal/stralth/hacking gameplay found themselves at boss fights that were straight-up gunfights. If you were kitted out and skilled properly to face-tank while using explosives and big guns, you were just screwed and couldn't progress.

In subsequent releases, they added additional options in the arenas that allowed you to kill them using stealth and hacking skills.