After using iTunes 11 for about a month, to give it a chance after my initial disgust (see this post), I couldn’t stand it any longer.
And, after weighing up various options, including various alternative players, I decided to downgrade to iTunes 10.7. iTunes 10.7 supports iOS 6 so I would still be able to sync my iPhone while enjoying all the features and aesthetics which are sadly (and annoyingly) lacking in iTunes 11.
I can confirm that by using this method my iPhone, which is currently running iOS 6, does not get the “restore factory settings” error and has no problems syncing and accessing all the apps I downloaded using iTunes 11.
I also did not get the dreaded error message (-42408).
I had both these problems when I tried to downgrade previously. So this guide also provides a solution to these errors.
I would also like to add that my iPhone is not jailbroken (just FYI).