Long alkyl groups are used in many functional polymers to improve their performance. The methylene sequences usually show a strong tendency to aggregate to form small alkyl nanodomains which can be either completely amorphous or partly crystalline. The influence of main chain packing, domain size, and density on the properties of self-assembled alkyl nanodomains is studied on the basis of a comparison of regiorandom and regioregular poly(3-alkylthiophenes) (P3ATs) with different side-chain length as model systems. We show that the dynamics of the CH2 units in amorphous alkyl nanodomains is mainly independent of the packing of the main chains. Relaxation spectra show a similar CH2 dynamics despite the fact that the thiophene main chains are crystalline in regioregular but amorphous in regiorandom P3ATs. The systematic dependence of the CH2 dynamics on alkyl nanodomain size without clear change of the average volume per CH2 unit underlines the importance of geometrical confinement. A competition of main- and side-chain crystallization mechanisms is discussed which should be considered if higher P3ATs are optimized for optoelectronic applications.