A 2003 study had participants defecate using a standard toilet seat (41-42 cm high), a lowered toilet seat (31-32 cm high), and while squatting. The results were that, regardless of toilet seat height, pooping while sitting took more time to completely empty the bowels, and required more effort to get it all out.
Further studies have indicated that all this extra pressure that we put on our colons when using a toilet is actually hurting us. In fact, the use of toilets increases our chances of developing ailments like hemorrhoids and diverticulosis (the formation of holes in the colon).
In the grand scheme of things, flush toilets are a relatively recent addition to our lives (having been invented in 1591). Though they clearly have bettered people’s livelihoods by improving overall sanitation, the fact of the matter is that the sitting position that toilets force us into result in anorectal angles (angle formed at the junction of the anus and rectum) that are less than ideal for efficient pooping. The angle is at 90 degrees while standing (keeping us from releasing at the wrong time) and only improves to 100 degrees when sitting on a toilet. While squatting the anorectal angle improves to 126 degrees, making everything flow much more easily.
Of course, as more people become obese, it becomes more of a strain to get into a squatting position and stand back up from a squatting position multiple times every day. Read more about the advantages of squatting in this Slate article.