Absolutely not. Both doxycycline and Malarone are as effective, if not more effective, than mefloquine. There's no area in the world that we send troops to where those drugs are not effective. In contrast, a large part of the world demonstrates some resistance to mefloquine.
As for questions about whether soldiers will be as compliant with a daily dose versus a weekly dose, these issues have long since been settled. When the U.S. military shifted from mefloquine as its preferred drug to doxycycline, and later to Malarone in 2009, we saw rates of malaria decline precipitously. As Dr. Ritchie alluded to before, this was because soldiers are, in general, compliant with their doxycycline and Malarone. With mefloquine, on the other hand, based on the guidance in the product insert, we should expect somewhere around a third of soldiers taking mefloquine to discontinue the drug in accordance with the product insert guidance. It's simply not a practical drug to use if soldiers are permitted to discontinue it in accordance with the label; they'll do it themselves and simply not tell their commander.
The U.S. military probably presents the best anecdotal example of the differential effectiveness of these drugs. In 2003, we deployed a few hundred marines on shore to Liberia for a humanitarian mission. Within a few weeks, the mission was scuttled. Dozens were evacuated with suspected malaria. They were all taking mefloquine, or supposedly taking mefloquine. Contrast that disastrous experience with mefloquine with our recent, very successful operations in Liberia. Thousands of personnel spent months in the very same malaria-endemic area, but they were taking the much safer daily drugs, doxycycline and Malarone. There were zero cases of malaria. I think that is sufficient evidence.