If you have an account you can set it to show up to 500 comments per page, and then you'll want to set it to sort comments by "best" (there's a drop-down for that on the comment page itself) - which if you just want to casually read a massive comment thread like this is usually better than "top" or any of the other choices.
And then hit "hide all child comments" - the nested comments are people having side discussions (explaining the joke, discussing variations) and there won't be new jokes there. Well, people will piggy-back on the popularity of another joke by replying to it with their own joke, but whatever.
I do agree that it's unwieldly, but it just takes some getting used to. I think it's the best system out there - it handles small discussion threads (as small as those on boingboing) as well as absolutely massive ones equally well (as well as is possible anyway).
But I stopped regularly looking at reddit half a year or so ago, and don't miss it. Massive time sink, and way too easy to get into arguments there