Personally I just think that Nihilus and Traya are bad bosses.
Nihilus is bad because his constant buff stealing makes you feel bad for getting any sort of buffs on your team. His constant health damage forces you to use a healer or something that does that job. His constant protection stealing makes it feel actively detrimental for some of your characters to attack him, which is especially bad when you've got no choice. His cooldown increases slow down teams, making them less fun to play and reducing synergy. And his Annihilate is inconsistent and, at times, impossible to predict.
Traya is bad because of Isolate. Only that. Everything else she does really doesn't matter. It's occasionally annoying, but altogether fine. Isolate ruins everything by making every team feel awful to play. There's not even any counter to it in P3. You just have to live with one of your characters practically not existing for a while.
Sion, on the other hand, is a fantastic boss. The constantly increasing offence on each side makes it a really tense game of trying to figure out how much damage you can squeeze out without getting someone obliterated because you didn't cleanse in time.