I have this issue on my iPad (first gen). I do not have a solution, nor does Apple. I have rebooted the device; Reset to factory settings and restored from a backup; Reset to factory settings and deleted all information; The Genius Bar at an Apple Store did the same and all they could do is shrug their shoulders and say, "shouldn't do that."
I can get apps to transfer via iTunes, but not via a wireless connection. Here's the odd thing. I have an iCloud account and tried to download an app on the iPad. I got the waiting icon. However, on my iPhone, which is working as it should the app downloaded flawlessly via the automatic iCloud connection. I'm wondering if there is something about the iCloud that is making it defective
Do you have another device, linked to the same iCloud account? when you try to download an app on the iPhone, does the other device download that app as it should?
I have an iPad (Gen 1) and iPhone 4. Both were connected to iCloud and to iTunes, although the login for icloud differs from the login for iTunes. The app download on the iPad was not functioning, the app was in constant "waiting" mode.
I fixed this by logging out of iCloud and iTunes (Store) on both devices, and powering off both devices. Then I powered up the iPad, the device that was failing to download, and logged into iTunes (Store) first. The download worked. Then I logged into iCloud and checked the download. Then I powered on the iPhone, logging into iTunes (Store), then iCloud , checking the downloads on each device, and everything worked.
Two other settings need to be checked. For all of these tests iCloud backup has been turned off on both devices. Plus, automatic downloads of apps, music and books in iTunes (Store) is also turned off.
If you only have one device, I suggest logging out of both iTunes (Store) and iCloud, powering off, powering on, then logging into iTunes (Store) first then iCloud.
Hope that works.