We don't have this problem 90% of the time in our campaigns; each GM knows that when it's their turn again, they can change rules as they see fit. Players will only make a fuss if the proposed change is just too far-reaching; for instance, all fighters lose bonus feats and have a poor BAB increase; magic doesn't work here, but there are plenty of creatures running around with DR 20/magic; or something similar. Mostly, other than the occasional feigned complaint, we're fine with a GM's house-rules, because the GM is still looking out for us to have fun.