If you are using aeroponics, the pot size won't make too much of a difference since the roots are growing ouside the pots pretty quickly. For hydro or soil, the pot size will correspond to the size of the plant, hence it will affect the total output. Pot size won't affect quality, so if you are looking to do a SOG, a smaller pot would be ok. Mothers should have larger pots to allow for quick regeneration of potential clones (larger root area allows for more vigorous growth up top).