I agree that changing to a higher fare class should not involve a change fee --- after all this is simply putting more money into the airline!
The one caveat would be with the "full fare" tickets. If you buy up to a full fare within 24 hours ... great. If you buy up to a full fare after 24 hours, it should be allowed without the change fee, however, it should not be refundable. Otherwise, people could buy non-refundable tickets, and then when they need to refund it, they could buy up to a Y class ticket and then refund.