<p>I noticed foot arches are already digitized, but custom arch supports are usually expensive.  PLA and ABS aren't the best material for printing arch supports, especially if they replace the shoe's innersole. </p>

<p>Is there a more flexible material for 3D printing that could be used for making custom orthotics?</p>

The standard choice for this would be TPU,
thermoplastic polyurethane
.
TPU is a common filament material for use in fused filament fabrication 3D printing due to the fact that it is an elastic thermoplastic which makes it ideal for printing objects that need to be flexible and elastic.
...
Properties of commercially available TPU include:
high abrasion resistance
low-temperature performance
high shear strength
high elasticity
transparency
oil and grease resistance
In addition to TPU, there are plasticizer-modified PLA filaments with similar flexibility, but not necessarily with the other nice properties like abrasion resistance. I've printed with one from 3D Solutech and had good results,
after figuring out what to do about stringing
.
Also, it's possible to achieve a decent degree of flexibility merely with printed geometry, rather than special materials. It's possible that PETG with an appropriate geometry could work for your application.