It really just depends on who is running the store and the district, it seems. I work at a Gamestop up in Western Washington, and all the time I hear complaints about some of our stores in neighboring cities, which prompts them to actually drive out of town to stop by us. [We are the largest store in our district, and we offer the best customer service we possibly can.]
I think that most Employees of our chain can be summed up quite well as a couple posts in this thread have detailed: Summer-job reject students, and just plain douches and jackasses who don't care.
Scenario 1: I completely understand you here on the wrapping, I myself will not buy a 'gut' copy of a game, as they are called. I bloody well even work there and I won't! For me, if a game is new, it has wrapping around it. End of story. So, if a customer ever does come up and we only have the gut left, I always check with them if that is okay with them, and if not, call around to a couple other locales and find one that has some sealed. You are entirely in the right here, so next time stand up and tell that employee that you don't give a crap what s/he thinks about the wrapping, just to make a call and look for one.
One reason for this, though the people at my store do not do it, is a little known fact. A perk of employment at Gamestop is you can 'check out' a game for up to 4 days at no cost. When a new game has been out for two weeks or more, an Employee can check out a NEW COPY of the game, not even a used one, but the very same copies they are telling you have 'never been played', and 'only been stored'. This is one reason I will not buy a gut.
Scenario 2: I can't find a 'logical' reason why an employee would swap the cases on you, but that's assuming that the workers at your particular stores have enough of a brain to actually have it oozing out their bung. Which it sounds like they don't. I end up always checking over the pricing of everything after it rings up at the register, and if there is a case like that, I will knock that sucker down without a moment's thought. It's the price that is marked, and it's the price they shall receive [unless it's lower, in which case savings for all!].
It just seems to me that you have to be in a decent area to have a Store Manager who hires competent people, and to find a decent District Manager who keeps up on his Store Managers and staff to make sure that they are helping the people that come to them. But I must agree, I think I've heard far more complaints out of mall stores then ones outside of a mail, such as there is one store I just flat out will not ever go to because their Store Manager is a royal [you'd like to know, wouldn't ya?], and I'll gladly tell people that too, since I get quite a few complaints out of that store.
Biggest thing: if you ever have a problem with your local stores, ask for their DM's number and give them a call. Don't just skulk out because some Games Associate [Really? We can't just call ourselves Sales Representatives?] was trying to see how far he could stuff a stick up his rectum before it bled and you interrupted with a question. Make something happen of it. If anyone tries to tell you that they "can not just hand out their DM's phone number", tell them to go to hell, and that it is the law that they must provide a line and capacity to file a complaint, of which a DM himself has logged against his stores and district, and must take care of themselves. As such, they generally would like to keep that to a minimum.
Go Customer Rights!