Prayer is with the heart, not with the head. Emotions are a source of energy, and can be directed toward desirable or undesirable goals. One can direct his anger toward other people, which is bad. Or one can direct his anger toward injustice, which is good. All emotions can be directed either positively or negatively.
Many emotions are self-centered in a way that is detrimental to spirituality.
The intellect must be put to work to turn the emotions away from physical desires toward spiritual concerns. Prayer, however, needs very little direction. As children we ask our parents to provide for our needs. To the contrary, it indicates that one realizes he is dependent on G-d for everything. Praying for what one wants testifies that one believes in G-d.