Sure foundation is by far the most ad-hoc axiom. But it is also one of the one's that is easiest to see doesn't generally matter. For pretty much any natural theorem if a proof uses foundation then there's a version of the theorem without it. Since not-well founded sets don't fit most of out intuition for sets as things like boxes that's not an issue. None of the serious apparent paradoxical properties go away if you remove foundation.
It's a very cool construction, but it's a finite one that we can verify by hand or with computer assistance. Of the things that ZF claims exist, some of them have this "verifiability" property and some don't. At the very least don't you agree that's a crucial distinction, and that we ought to be strictly less skeptical of constructible, computable, verifiable things than of things like uncountable ordinals?
Yes, certainly but by how much? If our intuition can go this drastically wrong on small finite objects why should I trust my intuition on objects that are even further removed from my everyday experience? I mean it isn't like I need 30 or 40 sided dice to pull this off. In fact you can actually make much smaller than 6 sided dice that are non-transitive. Working out the minimum number of sides (assuming that each die in the set doesn't need to have the same number of sides) is a nice exercise that helps one understand what is going on.
You're right, I see that it's the "restriction" of restricted comprehension that actually does the work in avoiding Russell's paradox, not foundation. Nevertheless, the story is the same: we had an ambitious set-theoretic foundation for mathematics, Russell found a simple and fatal flaw in it, and we should not simply trust that there will be no further problems after patching this one.
...If our intuition can go this drastically wrong on small finite objects why should I trust my intuition on objects that are even further removed from my everyday
Update: Discussion has moved on to a new thread.
The hiatus is over with today's publication of chapter 73, and the previous thread is approaching the 500-comment threshold, so let's start a new Harry Potter and the Methods of Rationality discussion thread. This is the place to discuss Eliezer Yudkowsky's Harry Potter fanfic and anything related to it.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven. The fanfiction.net author page is the central location for information about updates and links to HPMOR-related goodies, and AdeleneDawner has kept an archive of Author's Notes.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: