Inductors, like all electrical components, have limitations which must be respected for the sake of reliability and proper circuit operation.
Rated current: Since inductors are constructed of coiled wire, and any wire will be limited in its current-carrying capacity by its resistance and ability to dissipate heat, you must pay attention to the maximum current allowed through an inductor.
Equivalent circuit: Since inductor wire has some resistance, and circuit design constraints typically demand the inductor be built to the smallest possible dimensions, there is no such thing as a "perfect" inductor. Inductor coil wire usually presents a substantial amount of series resistance, and the close spacing of wire from one coil turn to another (separated by insulation) may present measurable amounts of stray capacitance to interact with its purely inductive characteristics. Unlike capacitors, which are relatively easy to manufacture with negligible stray effects, inductors are difficult to find in "pure" form. In certain applications, these undesirable characteristics may present significant engineering problems.
Inductor size: Inductors tend to be much larger, physically, than capacitors are for storing equivalent amounts of energy. This is especially true considering the recent advances in electrolytic capacitor technology, allowing incredibly large capacitance values to be packed into a small package. If a circuit designer needs to store a large amount of energy in a small volume and has the freedom to choose either capacitors or inductors for the task, he or she will most likely choose a capacitor. A notable exception to this rule is in applications requiring huge amounts of either capacitance or inductance to store electrical energy: inductors made of superconducting wire (zero resistance) are more practical to build and safely operate than capacitors of equivalent value, and are probably smaller too.
Interference: Inductors may affect nearby components on a circuit board with their magnetic fields, which can extend significant distances beyond the inductor. This is especially true if there are other inductors nearby on the circuit board. If the magnetic fields of two or more inductors are able to "link" with each others' turns of wire, there will be mutual inductance present in the circuit as well as self-inductance, which could very well cause unwanted effects. This is another reason why circuit designers tend to choose capacitors over inductors to perform similar tasks: capacitors inherently contain their respective electric fields neatly within the component package and therefore do not typically generate any "mutual" effects with other components.