I think Ancient Wisp has ended more runs, if only because it can be a pain to take care of if also dealing with a large mob on its level. Vagrant probably similar. They're both reliant on dodging their telegraphed but hard-hitting attacks, and if you're also dodging mobs, you may be a second short of dodging the boss, but a large mob can crunch your health just as quickly. I can't say much for the Core bosses; I only reached there once, but I was so overpowered that I ultimately just committed suicide to get my score that time, so they really didn't seem that bad, even when I had double Cremators.
In general, I don't think any of the bosses are terribly HATE-worthy, since they're all really predictable. I mean, hopoo said it already, but certain elite mobs have higher 'casting cost' as bosses, and you can get giant piles of those. Giant piles of enemies/enemy deathballs are the worst part of triggering the teleporters, particularly earlier in the game, especially if there is less room to kite easily. With the addition of missile mobs, kiting is even harder since you'll just get infinitely spammed by those missiles as you try to kite.
Now, if we're also taking into account boss piles... well, I actually rarely get multiple bosses at the same time anymore (hell, I rarely get them spawning on their own independently of the teleporter), and I think I've only seen four elite bosses ever (yellow vagrant, orange vagrant, green golem, blue worm). I imagine the contact-damage Vagrant, which I've only heard spoken of in hushed and terrified whispers, is the worst of the lot...
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