Let's skip past what we should be eating and make the positive assumption that our diets are pristine and perfect, the way God intended for them to be. What happens then? The perfect food that we're eating is swallowed and digestion begins. How well does the food we eat get broken down and absorbed the way it should? There are a large number of factors and interesting health issues over which we have some degree of control.
First is the act of chewing. In our hurried society it is all too common for us to fall into the "stuff and gulp" game, where we barely chew food in the interest of hurriedly getting to the next appointment. Chewing does two things: it manually breaks down food into smaller pieces and saliva (containing the enzyme amylase) begins the chemical breakdown. Try this for one meal: chew each bite of food 20 times before swallowing it. This will greatly reduce the amount of work the rest of your body has to do in order to extract the nutrients from what you're eating.
Next is the stomach. The stomach is a complicated, ingenious organ. It can produce acid at a pH of less than 3, while at the same time protecting itself from dissolving along with the food eaten. As we age our stomachs produce less acid, so the chemical breakdown gets impaired leaving larger pieces of food that can't be readily absorbed farther down. Stress and exposure to various toxins and bacteria can reduce the amount of protective mucus that gets produced, reducing protection of the stomach wall. Ulcers and heartburn are just two of the common stomach conditions caused by poor acid and mucus production in the stomach.
The degree of stomach acid produced sets the tone for the rest of the functions in the digestive tract, the next one being up to the pancreas. Strongly acidic food entering the duodenum triggers the pancreas to release clouds of sodium bicarbonate and digestive enzymes. Enzymes do the bulk of the digestive work by preparing the smallest particles for absorption. Proteins are broken to amino acids, carbohydrates are broken to simple sugars, fats are broken to fatty acids. These smaller molecules can then pass through the intestinal walls into the blood stream and be utilized at the cellular level throughout the body. Enzymes can't function in an acidic environment, so the bicarbonate is crucial. If acidic food remains in duodenum it can burn the lining since there are far fewer mucus producing cells in the duodenum. If the food is not that acidic coming into the duodenum from the stomach the pancreas won't release as many enzymes and whole proteins, carbohydrates, and fats will pass through the digestive system without being absorbed.
Most of the absorption that takes place occurs in the intestines and colon. Friendly bacteria live there to help with absorption and/or to keep the pathological disease-causing bacteria in check. Different places throughout the 20 some feet of intestine absorb different nutrients.
So, in summary: You can eat a perfectly balanced, nutritionally dense meal and it can be compromised by poor digestive function. If you have digestive system symptoms it is good to get them checked out. You may not be making enough acid (about 80% of time this is true), or enough mucus, or enough digestive enzymes, or sodium bicarbonate, or have enough friendly bacteria. All of these deficiencies can be corrected through supplementation.