Paragraphs separated by a couple of line-breaks do not need auto-indenting whereas those paragraphs which are not separated do need auto-indenting. It's all down to use of the written language.

Certainly in English a paragraph should never be indented if paragraphs are separated by a blank space. This is how I was always taught and every text book or article I have read follows this pattern. Perhaps the only exception would the very first paragraph of an article. This would then be done using CSS within the theme's stylesheet

For example:
#article:first-line {margin-left: 10em;}
This would indent the first line of an element with the ID of 'article' by 10 spaces - each space being relative to the font size currently in use.

Any non-indented paragraph is very hard to read.

PS: neither the Wordpress Ideas script is too great. It doesn't even allow paragraph indenting