The enhancement of the extraction efficiency in light emitting diodes (LEDs) through the use of photonic crystals (PhCs) requires a structure design that optimizes the interaction of the guided modes with the PhCs. The main optimization parameters are related to the vertical structure of the LED, such as the thickness of layers, depth of the PhCs, position of the quantum wells as well as the PhC period and fill factor. We review the impact of the vertical design of different approaches of PhC LEDs through a theoretical and experimental standpoint, assessing quantitatively the competing mechanisms that act over each guided mode. Three approaches are described to overcome the main limitation of LEDs with surface PhCs, i.e. the insufficient interaction of low order guided modes with the PhCs. The introduction of an AlGaN confining layer in such structure is shown to be effective in extracting a fraction of the optical energy of low order modes; however, this approach is limited by the growth of the lattice mismatched AlGaN layer on GaN. The second approach, based on thin-film LEDs with PhCs, is limited by the presence of an absorbing reflective metal layer close to the guided modes that plays a major role in the competition between PhC extraction and metal dissipation. Finally, we demonstrate both experimentally and theoretically the superior extraction of the guided light in embedded PhC LEDs due to the higher interaction between all optical modes and the PhCs, which resulted in a close to unity extraction efficiency for this device. The use of high-resolution angle-resolved measurements to experimentally determine the PhC extraction parameters was an essential tool for corroborating the theoretical models and quantifying the competing absorption and extraction mechanisms in LEDs.