Composite solar cells based on conjugated polymers and fullerenes represent an attractive platform for organic photovoltaics. Blends of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl C61-butyric acid methyl ester (PCBM) show state-of-the-art performance, with efficiencies approaching 5%. While polymers with more optimal electronic structures than P3HT are known, enhanced performance is generally not observed due to the less than optimal blend morphology that is generated in fullerene-composites. We have made efforts to gain a deeper understanding of the polymer structure-function relationships in P3HT in order to establish fundamental principles for extension to polymers with more optimal electronic structures. Specifically we have focused on polymer regioregularity in P3HT as well as the alkyl substitution pattern in poly(3-alkylthiophene) copolymers. The synthesis of novel poly(alkylthiophenes) will be described along with the strong influence of alkyl substitution pattern and regioregularity on the thermal stability of the composite active layer.