Onyx already is interesting enough. It just lacks the "chambers" atm, the sewer design is fine. And as said, the respawn and resspad logistic is plainly awful.
Rare bosses could be linked to items that summon them. Those items could drop randomly.
Hard modes can be triggered by different items or combinations...the "gates" inside onyx even offer for links to badass other dimensional fights...
Also it can serve as a hub (sewers after all) passage to black ring non raid instances or another stygian themed scaling instance.
Oh...and open up Hakar-Teps Den of Perversions to all independant of quest, please. The basic idea of instances in an instance is good, but that quest dependancy spoils everything.