The supreme missions could use some extra challenge. If you do encounter a boss its an open field one that's a straightforward bullet sponge event.

Dark souls changed peoples expectations when it comes to bosses and challenges, while this is a different genre, a lot of the challenging aspects of soulsgames can be adapted. An addition of a boss room, will allow you to add more rotations in boss attacks, environmental hazards that pose a challenge, and a better implementation of teamwork mechanics. 

Environmental Hazards can be time/phase based. Boss attack rotation or phases can switch between AoE, column, cone attacks that must be avoided, one hit kill attacks etc. The diablo 3 Butcher room is a great example of environmental hazards, and how a boss room adds to the challenge. Also different bosses can have different mechanics that add to the challenge.

Classes can have the option to fulfill tank, dps, support roles, and further enhance the teamwork experience, as well as allow you to come up with all kinds of challenging boss mechanics that require strategy and teamwork.