It happens with some of the bosses that their behavior changes when you destroy parts of them. I think both a game mode and a mutation could be based on this, al a Elite Enemy and Bravado.
The way fracturing enemies as a game mode could work is that when the main hull is destroyed, there is an increasing chance that enemies will break apart and continue to fight you with other weapons, such as individual bursts of flak (1 projectile, instead of 18) if the part used to be main hull or armor and maybe the swarm beam weapon if the part used to be a power plant. The associated mutation would change this from a scaling percentage chance to flat out 100% like Bravado.
Let's say that fragments, if they spawn, spawn with 10% of the original hull points of what they came from. Instead of starting them with a new health bar, they would start 10%; meaning that they could eventually heal up all the way. Also, this would make the Terminate mod very valuable, as fragments would be disable.