Please show me a reflowable document with decent typographics. No, seriously, why browsers don’t implement fully-featured layout algorithms? Until then, I’d prefer a well-typeset PDF over an average website for a longer-form and graphics-rich content.
Also, those are naturally usable offline, are durable and have no interactive annoyances.
Hmm, do you have any more specific examples of typographics being a deal breaker ?
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 ?)
Also, those are naturally usable offline, are durable and have no interactive annoyances.