We investigate the behavior of three-dimensional (3D) exchange-correlation energy functional approximations of density-functional theory in anisotropic systems with two-dimensional (2D) character. Using two simple models, the quasi-2D electron gas and two-electron quantum dot, we show a fundamental limitation of the local density approximation (LDA) and its semilocal extensions, generalized gradient approximation (GGA) and meta-GGA (MGGA), the most widely used forms of which are worse than the LDA in the strong 2D limit. The origin of these shortcomings is in the inability of the local (LDA) and semilocal (GGA/MGGA) approximations to describe systems with 2D character in which the nature of the exchange-correlation hole is very nonlocal. Nonlocal functionals provide an alternative approach, and explicitly the average density approximation is shown to be remarkably accurate for the quasi-2D electron gas system. Our study is not only relevant for understanding of the functionals but also practical applications to semiconductor quantum structures and materials such as graphite and metal surfaces. We also comment on the implication of our findings to the practical device simulations based on the (semi)local density-functional method.