The choice of aperture size depends the science. The constraints revolve around the lipids used, the difficulty in incorporating a channel, and the channel's kinetics.

Generally, speaking the smaller the hole, the lower the capacitance noise in the system. The result of which is the ability to resolve faster channel kinetics at a lower current amplitude. However, the smaller the hole, the harder it is to get a channel into the membrane.

As a rule, you want to work with the smallest membrane possible. Many researchers report membranes having a capacitance of 80-120 pF achieve a good balance between noise and time-to-incorporation.