I love it when some people start panicking over news which is totally unsubstantiated.
First of all that article has no mention whatsoever of how they tested the flake food and their results. Was it a study, experimentation or simply somebody's “opinion” that flake food lead to malnutrition?
The companies, who produce flake food, must be quite aware of what their products contain, and they must have tested it--simply because their business depends on it.
Fish are first and foremost "cold blooded", meaning they're not like us or the rest of mammals which need a varied diet rich with proteins and other components to keep up with their metabolism. Cold blooded animals have a different metabolism and they can store food energy for a long time. The temperature in their environment decides how faster or slow their metabolism works.
When fish are fed flakes, the nutritional aspects of flake food get accumulated after many regular feedings... no doubt that a varied diet will help the fish; however, it should also be remembered that one cannot just dismiss one of the factors which allowed tropical fish to be kept in tanks -- flake food.
Some snakes (not fish but very similar) can go without food for a whole year after one hearty meal… personally I have seen sick fish survive without food for a whole month!
So the bottom line is that every bit of news should not be taken as absolute truth.