Portal SPOILER WARNING!!!!
Boss fights need to be more creative, think about how great it was in Portal. You use the gun to get the boss to shoot itself, it drops a limb/organ, you then portal to to open a hatch to drop the organ into, Each time acquiring the limbs were different as well.
Boss fights in MMO's are great aswell, Sometimes the lead up to a boss fight was more fun than the boss itself. An example is in WOW when you fought in the Suppresion room in Black Wing Lair, or the Vael fight with infinite mana/energy/rage.
When a boss fight is outside of the normal tank and spank or shoot first to win scenario, they can be extremely fun.
In rail shooter games, when bosses have 1 weak spot that can be exposed by hitting another, even though its rinse and repeat when the stages change of the boss, it becomes challenging to maintain focus.