All drugs have some side-effects, and based on my experience, Malarone is the best. The 3 drugs that I've been prescribed for diving in malaria zones are: Malarone, Doxycycline, and Lariam.
Doxycycline increases sun-sensitivity, and while I've used it, it was a bad choice while on the equator and constantly exposed to intense water reflection and sun. None of my dive group uses it.
Lariam is known to cause neurological and psycholgical symptoms in some people, and as of last year, carries a 'black box' warning from the FDA. Most of us had mood swings on Lariam, some found it unpleasant.
Malarone has been known to cause vivid dreams in some people, but when I do a live aboard, those that are taking anti-malarial drugs are always using Malarone, and no one complains about it.
Hope this helps,
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