Methods for optimizing, designing, making, and assembling various component parts and layers to produce optimized MEAs. Optimization is generally achieved by producing multi-layered MEAs wherein characteristics such as catalyst composition and morphology, ionomer concentration, and hydrophobicity/hydophilicity are specifically tuned in each layer. The MEAs are optimized for use with a variety of catalysts including catalysts with specifically designed and controlled morphology, chemical speciation on the bulk, chemical speciation on the surface, and/or specific hydrophobic or hydrophilic or other characteristics. The catalyst can incorporate non-platinum group metal (non-PGM) and/or platinum group metal (PGM) materials.