Cutting costs and improving quality are things that smaller studios try to do to compete with larger stop motion companies like Aardman and Laika. Much like any industry that uses automation, it is a sad reality that comes with trying to increase profits for the sake of keeping a company alive for the next project. There are definitely philosophical points a person could make about it, particularly how 3D printing and digitally creating characters goes against the grain of hand crafted traditions. This is what separates business from the hobby world and there are good reasons to take both approaches.
Motion Foundry Studios is working on an ambitious feature film called Saurus City that has some high grade voice acting and a small team of dedicated artists. To lower costs and speed up production they created hybrid puppets that use both 3-D printed heads with replacement mouths and hand made bodies and armatures. They had their parts printed by GoEngineer, a company that has high end 3D printers capable of printing parts in color. The are one of the few companies that have experience making stop motion parts specifically for the industry. If you'd like to learn more about them you can visit their site by clicking here.