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One huge downside to disabling the importing of HTML files and storing them as ZIP files is that you lose any external files referred to by the HTML file such as style sheets, images (covers), etc. It also only works if there is a single HTML file, not a series of linked ones for different sections of the eBook. The default Calibre import of HTML parses the HTML during the import and adds these to the zip file it creates. Since a large proportion of eBooks tend to have these additional files it is definitely something to consider when making a choice to store just the HTML file. You also lose the compression of the HTML (which can be anything up to 90% reduction in size for HTML) although I suspect most people are less concerned about that.
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