Simple, just like we have that troll in ac, you put diffrent random encounters and even challenges (not only simple boss fights, diffrent things like in fotm) in dungeons so it won’t be so boring repeating them.
Also you can introduce bonus challenges that gives you extra reward (like in shaman fractal that chest if you save all prisoners) this could help with skipping/exploits problem too if it’s done right. What do you guys think?