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Substrate-type planar 2-D photonic crystal (PhC) waveguides suffer from large experimental propagation losses compared to membrane-type PhC waveguides. Numerical simulations can give insight into the quantitative contribution to the propagation losses originating from fabrication imperfections and nonideal designs of the waveguide or the vertical layer structure. Many numerical studies have been performed in the past addressing only a part of the question. All of them lack the general overview, which is essential to identify the main source for the large propagation losses. Since those studies are performed with various numerical methods on many different PhC waveguide designs, a general overview cannot be reliably assembled from the literature. Therefore, we (re-)performed a comprehensive set of numerical experiments with the 3-D finite-difference time-domain method to investigate the influences of imperfections, such as the finite etch depth, a conical hole shape, the finite number of lateral layers of holes, the asymmetric vertical layer structure, lattice disorder, and variations of the hole radius. A major result of this paper is a list of requirements to be met by the process technology for the fabrication of a W1 PhC waveguide in the low-index contrast system (InP/InGaAsP/InP). Furthermore, we were able to identify the angled sidewalls to be responsible for the main fabrication-related propagation loss contribution. Finally, we show the potential of new, alternative low-loss waveguide designs for the weak index contrast system and emphasize the importance of using realistic hole shapes in this search process.