All of these are potentially good points if they're backed up by a valid design reason (as opposed to a personal preference or opinion). I always caution against fixed ideas that might not apply in every circumstance.
For long documents, readability, invisibility (making the typography unnoticeable), clarity (chapters, headings, subheads and text clearly indicate the hierarchy and relationships of information) and avoiding reader fatigue are the most important considerations. Making it beautiful is terrific, but only after those points are covered.
Maintaining even type color, low contrast (lighter and serifed rather than heavier or sans-serif typefaces, and type that is not too densely packed) and a measure (line length) not longer than 2 to 2.5 times the length of the lowercase alphabet are all well-proven guidelines.
Justified Text: I've yet to meet a designer, and I'm sure I'll never meet a typographer who's against justified text in principle. There are almost two thousand years of typographic and calligraphic tradition to the contrary.
In word processors, the only available means of achieving justified text is to adjust word spacing. Because we hate rivers and random blobs of white in text, this tends to make designers develop eye-tics and mumble dark thoughts into their margaritas. Sadly, perhaps, this is akin to bad kerning: non-designers almost never see this until it's pointed out or it's truly glaring.
We tend to forget that justification-by-word-spacing was the norm in newspaper, magazine and even book typesetting for most of the period from Gutenberg until the advent of digital typography. Finely letter-and-word-spaced justification was done, but it was very labor-intensive and therefore expensive. Take a look at some 18th or 19th Century books to see just how awful it could and did get.
Unless the measure is too short, forcing dreadful word spacing, justified text can look more inviting and create a more professional impression than ragged right, especially if one pays a bit of attention to hyphenation. Sometimes justification is necessary to create the look that the intended readership expects or will respect. By contrast, I know of at least once case where hyphenation was verboten for a series of long documents, and in that case justified text would have been a visual train wreck. So while "Don't justify text in word processors" is good advice, it certainly isn't a hard rule.
Point Size: Point size and line length are related. X-height and legibility at different sizes are related. Point size, measure, x-height and leading are interrelated. These relationships all affect type color, contrast and readability.
To say "You should never use 12 point type" is nonsense. For one thing, it depends how the document will be viewed and who will be reading it. If it will be desktop-printed on a standard office laser or inkjet printer, going below 10 point is risky. The resolution of the text is at best 600 dpi, so the character outlines are more and more affected the smaller the point size, which in turn affects eye-fatigue on long passages of text. Depending on the typeface, you might require 12 point. Garamond sets larger than, say, Century Schoolbook.
Margins: Deciding on a typeface, point size, line length, number of columns and gutter width determines the left and right margins, which are a matter of where you place the text block on the page. James Felici points out in "The Complete Manual of Typography" that word processors and page layout programs work backwards: first you set the page size and margins, then you set the columns and gutter, then you end up with a line length rather than determining it first.
One doesn't change margins in order to "make the document look more dynamic." Even if that were a meaningful statement in itself, most long documents are perfectly content to just sit there quietly, and most readers prefer things that way. There are only two reasons for margins: to make the document more inviting and to make it more readable. Margins derive from line length, so in almost all cases Word's defaults are, indeed, wrong and must be changed, but the reasons aren't relate to dynamos, the alignment of Saturn or what George Clooney had for breakfast. Where you place the text block on the page is a practical choice first, then an aesthetic one.
Font Choice: Changing fonts... I don't disagree, but you give no reason. Quite by chance, I blogged on this exact subject the other day, in a post directed primarily at business people but relevant to any discussion of MS Office. In summary, Times Roman, because it's been default for so many years, says, "Hi! I couldn't be bothered changing the defaults in my word processor." It's also drawn for use in narrow columns, which applies to very few such documents.
Calibri, the current default, is too high-contrast for long documents. Like most sans serifs, it tends to glare and become uncomfortable to read. Helvetica is downright painful after a couple of pages. Calibri Light would be a decent choice if you must use a sans.
Leading: Changing the leading "so it works" is easy to say, but far too vague to be useful to anyone but a designer or typographer. "Works" for what? Far better to explain that opening up the line spacing makes the page appear lighter and less intimidating to the reader, and helps prevent the reader's eye from skipping a line when scanning from the end of one line to the beginning of the next.
Hierarchy: As @MarcinWolny pointed out, all that's for naught if you screw up paragraph divisions and, I would add, headings.
In long documents particularly, the information hierarchy much be clearly expressed. Headings and subheads should be in contrasting type and/or spaced in such a way that they clearly separate the text and are adjacent to what they refer to (as opposed to mid-way between two paragraphs, which is a common mistake). Paragraph breaks must be clear, and not accomplished by adding extra blank lines. In non-justified text this is often helped by spacing rather than a first line indent. The reverse is true for justified text. Neither of these is hard and fast, by any means. As long as the paragraph separation is easily identified, the purpose is accomplished.
