When Pokemon Go was first launched, avatar customization was somewhat limited compared to other games. However, recent large updates to the game suggest that more options are on the way. Fansite The Silph Road has been datamining the updates and found hints of new customization options.
Specifically, The Silph Road has found graphical resources for customizable hair, eyes, shirts, pants, shoes, hats, and backpacks.
As to how these resources will be made available, the data miners have found several keywords related to the options, such as “new,” “sale,” “purchasable,” and “unlockable.” So it appears that some of them may be made available through the in-game store, while others could be unlocked by winning medals and completing achievements.
Niantic has not confirmed the existence of new avatar options, however, and has not given a time line for implementing these changes.