All fair points in many contexts, but not
all contexts. Some counters:
1. You can embed CSS easily, and images using data: URIs...
2. ... so you can download the whole thing as a single and work offline.²
3. Non-standard clients are not my problem, file under “you can't please everyone, especially those who chose to be difficult to please!”. Accessibility is a concern though, I'd need to look into that before using such techniques without a reliable fallback.
4. This isn't practical for sites/pages needing large resources like high-res images, or that are large generally¹, but not all sites/pages need large resources or are large in general.
5. Not everything needs to be indexed well by search engines, I have things out there that are only relevant to those I refer to them, though I agree this could be a significant issue for many.
6. True. Though that breaks your second point, so you need to choose.
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[1] you wouldn't want wikipedia done this way!
[2] also with external resources almost all browsers will happily save then when you do file|save, and to be pedantic the description given is “in a single html file” not “in a single file”