Also, those are naturally usable offline, are durable and have no interactive annoyances.
MHTML (aka .eml) is usable offline too (except for some reason by Firefox ?!?), while PDFs are horrible on screens smaller than the width of a page.
I'm not sure what interactive annoyances on scientific websites you're talking about - the most problematic ones these days are those with the assumption of a working Java or Flash plugin (and if they start to be plagued by irrelevant scripts it's much easier so far to block JavaScript in a browser than in a pdf reader), meanwhile many pdf readers don't even have any animation support, which is about content rather than presentation ! (As a metaphor : would you support a format unable to show pictures ?)