See here for a screen recording I created when trying to update my iOS apps after about a week from the last update.
Blogger was supposed to show a video box here,
but that doesn't seem to work.
Admittedly I am suffering from iTunes 11 more than most users because I have two iTunes accounts: A German and a U.S. account. And I have downloaded iOS apps from both accounts. This leads to iTunes wanting to update all apps for both accounts at the same time, even if it only shows me the German updates.
However, before iTunes 11, this was still manageable. iTunes 11 made this much worse.
Also, there are other alerts in there that even the usual Apple customers with just one iTunes account might experience, such as the late-appearing "age restriction" notice that pauses downloading, and messages about problems with particular apps without naming those apps.
Overall, iTunes 11 does this all plain terribly. Apple used to excel at good user interfaces. Nowadays, I get the impression they take the kids right from college, let them work on these programs with no supervision from anyone who still has a clue about how to avoid such bad user experiences.
(I've also reported this to Apple via their bugreporter, see http://www.openradar.me/15350892)