The incredibly minor things that have irked people in this thread has been pretty amazing to me. I mean, the packaging is indeed something to be somewhat upset about, but there's been some pretty memorable rage going on, especially a few pages back. The anime vs. CGI portraits discussion was a lot of fun
In the case of the...case...I think if the packaging ends up making people worried about the safety of the discs, then it's a real problem. As much as the stacked case sucks, I don't think it'll affect the discs in most cases. Hell, if discs can survive in paper sleeves, they should be OK stacked.
Now, the annoyance factor is a different story...especially considering the possibility of swapping that third disc late in the game.