I have no desire to be alarmist, but I think it is important to note that Crypto and Giardia are the best known eukaryotic parasites in surface waters but not the only ones.
I study the protozoan parasite Toxoplasma. Toxoplasma oocysts cannot be killed by any chemicals that are safe to drink. After 24 hours in 6% bleach (twice the strength of the stuff in the bottle at a drug store) they are 100% viable and readily cause fatal infections in mice. In my lab, we store viable Toxo oocysts in sulfuric acid. Many human infections have been reported from ingestion of water contaminated with this parasite. In 1995, about 400 people in Victoria, BC became infected from municipal tap water (which was chlorinated). Subsequent research found that the source was toxoplasma-infected mountain lions living in the areas around the municipal reservoir. The parasites were being transported in the watershed. In some areas in California, the proportion of the mountain lion and bobcat population that has the infection approaches 80%. In humans, toxoplasmosis (like cryptosporidiosis) is typically a long-term subclinical infection following an initial bout of GI symptoms. However, it has also been implicated as a risk factor for schizophrenia and cognitive changes, and it is a serious risk to a fetus if a woman becomes infected while she is pregnant.
Cysts of eukaryotic parasites (worms and protozoans) are probably in all backcountry surface waters (excluding direct snowmelt) because they are shed in huge numbers by many wildlife species and (in contrast to bacteria and viruses) they accumulate because they are extremely tough and remain viable for months or years in water and soil. Polyparasitism (concurrent infection with multiple parasites) is certainly the norm in people in many developing countries now, and it was probably the norm among people in the US until about a century ago. On the American frontier, everyone probably had parasites, and people who continue to drink untreated water when backpacking probably have them as well.
In remote alpine areas with fast-moving streams (at the top of the watershed), the risk from pathogenic bacteria or viruses is minimal, so a large pore filter (like the Frontier Pro) is enough by itself, in my opinion. In areas lower down on a watershed, but still remote, a small pore filter (<0.3 microns) is probably adequate by itself (removes worm eggs, protozoa, and most bacteria). In lowland or coastal areas, or areas regularly used by other hikers or domestic animals, it seems to me that there are only three good options: boiling, steripen treatment, or a combination of filter+chemicals. In these higher-risk places, filters alone are risky because they don't remove viruses or small bacteria (ie, Lepto, Brachyspira, etc.), and chemical treatment alone is risky because it won't inactivate some protozoa.
I use a Sawyer Squeeze or a Sawyer gravity filter and carry Aquamira tabs. I can use the Sawyer alone in remote alpine places (and I have the Aquamira tabs in case the Sawyer freezes), and in lowland places I use both (and wait 30 minutes).