The most destructive behavior is the default Look & Feel settings. If you uncheck "Remove spacing between paragraphs" and the "Insert blank line between paragraphs" settings, Calibre will leave most formatting as-is.

These settings can be useful in cleaning up badly formatted files, but should not be used carte blanche on all input files, especially those that don't have problems. You'll lose niceties like the first paragraph in a chapter not having text-indent, etc.

Generally it's better to use the "Edit book" feature on EPUB files and manually fix up the CSS if the styling is not to your liking. Converting with Calibre also hard-codes @page margins which overrides most e-Ink reader software's margin settings; so if I do end up using Calibre to convert to EPUB, I always have to edit it afterwards to remove these hard-coded margins in the CSS.