You can change the shell of user user in a template to /usr/bin/fish, it will automatically propagate to all AppVMs using that template.
This should look like this, after you installed fish in the template:
sudo usermod -s /usr/bin/fish user
I have this salt snippet for that
user:
user.present:
- shell: /usr/bin/fish
- groups:
- user
- qubes
With salt, you have to list the groups otherwise they are removed, see Changing user's shell with salt - #11 by unman