How could I make alt-shift skip the rarely used language(s)?

I would assume you can not. The system does not count keyboard lay-outs used to determine how often it is used.

Then again it becomes possible if you change the question to ....

How could I skip the rarely used language(s)?

Then the answer would be: by using another key combination and change that key combination to switch between the 2 lay-outs you do want to switch between.

Lay-outs are numbered from 0. So the 1st and 2nd lay-out are activated with respectively...

$ gsettings set org.gnome.desktop.input-sources current 0

$ gsettings set org.gnome.desktop.input-sources current 1

(or "2" if you, in your case, need the 3rd keyboard).

This will take up 2 keys though: you can add one to a key like control + P and the other to control + O. If you want this to be one key you would need to change the 0 in

$ gsettings set org.gnome.desktop.input-sources current 0

to a variable that toggles the 0 to a 1 and a 1 to a 0.

That would be this command:

gsettings set org.gnome.desktop.input-sources current $(($(gsettings get org.gnome.desktop.input-sources sources | grep -Po "'[[:alpha:]]+')" | wc -l)-1))

This would allow you to use 1 key and make it a toggle.

Refer to How can I change what keys on my keyboard do? (How can I create custom keyboard commands/shortcuts?) on how to set this. Tweak tools and compiz action plugin would be 2 methods on setting those.