I assume that such per-user options are now clashing with the new page caching optimizations in the mail archive (unlike the rel=next links which can be baked right into the cached page and therefore still work). Since they don't work anymore, it's probably better to remove those features altogether, than having misleading options in the user control panel.

Besides, nobody else seems to need those features. It's not right to burden you and the site with features that clash with its design just because of me.

For what its worth, I found a workaround for "expand quoted text by default" by simply disabling JavaScript for the kerneltrap.org domain. As for the message-ids, I think it's safe to say I will survive without them :) (especially since the bugs and missing messages are becoming rare in the mail archive).

I really appreciate the effort you've put into those features, but it does look like the drawbacks outweigh the benefits.