One of the main reason Omega-3 fatty acids (EPA & DHA) of marine origin are usually prefered is that the main ingredient, ALA,in flaxseed oil, is poorly converted into EPA & DHA in the body:
http://www.omega3sealoil.com/Chapter4_3c.html
An other practical reason is the more delicate conditions of storage & limited shelf life of flaxseed oil.
More reasons are provided in the above link.
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