Out of their more recent games, I think the boss fight I enjoyed the most was actually the King of Shadows in NWN 2. The game itself wasn't too great (although the expansion was good) but having multiple boss phases with different mechanics you had to react to was actually a significant step up from anything in Pillars. Too bad the fight wasn't actually difficult, but it had the potential to be with numbers tweaking.
I've always found these sort of boss battles a bit ...MMOish for lack of better word. I've always preferred bosses who have unusual or stronger abilities and smarter AI, perhaps coupled with an unusually tough selection of minions at their disposal. Having distinct phases is a bit game-y and, if not requires, then heavily encourages repetition of actions to get through a phase. I've found PoE's bosses to have the right idea, just not the best execution, especially when it comes to AI or the system in general. Many of this franchise's bosses rely on a single trick to surprise you with, but given how the system actually works, i.e. being able to stack defenses and ignore mechanics because of it, it wasn't very successful. It's no wonder people cite early-game bosses as some of the toughest in the games, like at-level Raedric or the Drake fight in the ruins; you can't stack defenses so high to be virtually impenetrable and to shrug off enemy abilities. I guess there are some builds in PoE2 that can do that, like the aforementioned Paladin/Wizard that relies on Wizard's Double, but that just proves my point how you have the possibility of manipulating the system to ignore encounter design, it just depends on at what level or build we are talking about.
From what people have been saying about super bosses, they kinda sound like JRPG (bonus, optional) bosses where the trick is to find a way to outlast the humongous HP pools than anything else. That's not bad in of itself, that can be a nice challenge once in a while, but copying it for every boss is lazy and boring. It's also not bad for some bosses to have phases once in a while, maybe not at certain % HP, but seemingly at random, so you can't always be prepared for the next phase just before it happens. I guess my point is that well thought-out boss encounter design that logically combines (and exceeds) the toughest challenges faced by the player up to now is the best case scenario, while at the same time having some variety to spice things up a little and catch you off-guard.