Yes, a 0.2 micron filter won't remove 100% of lepto. A 0.1 micron filter won't completely remove lepto, either. We use 0.1 micron eluate to inoculate lepto cultures if we need it to be very clean. Filters with 0.1 and 0.2 micron pores also won't completely remove Brachyspira, mycoplasmas, or viruses. There are some good arguments in the recent literature that intestinal colonization with Mycoplasma pneumoniae might be a component cause in some cases of Crohn's disease, inflammatory bowel disease, and colon cancers.
Viruses, spirochaetes (like Leptospira and Brachyspira), and mycoplasmas just can't be removed by any filtration method that is practical in the backcountry. When I hike in heavily used areas, lowland areas, areas that might have agricultural runoff, or areas that permit dogs or ungulates, I use iodine or aquamira in addition to filtration (the chemicals alone have questionable efficacy against Crypto). A good prefilter followed by thorough Steripen irradiation is really the only way to knock out everything, and I just don't think that is necessary in most alpine areas...yet.
Also, unlike protozoan cysts/oocysts and viruses, most prokaryotic waterborne pathogens (including spirochaetes and mycoplasmas) are not free particles in the water. They are almost always entrained on surfaces (often in biofilms). A study in India found that people could significantly reduce their risk of contracting cholera by filtering their drinking water through a piece of cotton clothing. The spaces in the fabric are much larger than a V. cholerae cell, but most of the bacteria in the water are adhered to larger particles that can become trapped in the cotton. So, filtration almost always achieves much better reductions in the burden of bacterial pathogens (not viruses or protozoans) than lab testing would suggest.
Both 0.1 micron and 0.2 micron filters will remove all protozoa and all common bacteria. The vast majority of spirochaetes and mycoplasmas will also be removed by both kinds of filters, and the small numbers that would get through (if someone encountered any) will probably be far below the minimum infectious inoculum. Viruses will pass readily through both kinds of filters. Given this, and the extraordinarily low prevalence of human pathogens smaller than 0.2 microns in alpine surface waters, there is no practical difference between the performance of 0.2 micron and 0.1 micron filters.
Ryan and Mary, This post was a bit wordy, but I don't mean it as any kind of rebuttal. You made a good and interesting observation, and my response just reflects my interest in it. I just think the pathogen burden in backcountry surface waters is a fascinating problem. It happens to be right up my alley.