Fish oil is superior in most capacities due to the fact that it contains un-conjugated fatty acids. Flax oil is mostly CLA, or Conjugated Linolenic Acid, which the human body does not utilize as efficiently.
Fish oil also comes closer to optimal 3/6/9 ratios.
Flaxseed oil contains ALA/LA but
not CLA. CLA is primarily derived from sunflower oil when it's in supplement form (in food form we can get it through meat and dairy), so the only way a flax oil would contain CLA is if the brand has sunflower oil added into the flax.
We can utilise CLA if that's what we are taking in else there would be no benefit to taking CLA supplements (and we know the studies confirm they are effective for fat loss), it's just that we can't convert ALA into CLA like some animals can. Is that what you were meaning?
Fish oil is
just omega 3 (with the omega 3 fatty acids being EPA/DHA) ~ it's the flax oil that covers the 3/6/9. Omega 3 is more important for overall health as we tend to consume enough omega 6 through our diets. Omega 3 is anti inflammatory whereas omega 6 is pro inflammatory, increasing the production of inflammatory chemicals known as eicosanoids.
I had an article published last year which goes into a lot more detail if you are interested:
http://www.thestrengthagenda.com/2012/09/13/the-importance-of-omega-3s/
Cheers MF.