Can't you just not sync apps and uncheck auto sync new apps ... or am I over-simplifying the problem? Or, would syncing apps, unchecking auto sync new apps and checking only iPhone apps get what you want?
In iTunes > Apps sync settings pane you'll see this, right below the home screen representation:This is driving me nuts and I can't find any direct solution to the problem, so I'm going to try and ask the question a little different than the OP. (Same issue as OP)
Is there a way in iTunes to not automatically sync every fricking app that is in my iTunes library??? Everytime I try to sync my iPhone, hundreds of apps, all of which are in my iTunes Library (Not New Apps) on my mac try to sync to my phone, which can't store them all even if I wanted to install all of them. This prevents me from installing old backups and from installing software updates properly if my phone is near max capacity for space.
iTunes has options to only add music and videos manually or from checked selections, so why are the Apps automatic no matter what I select in App options?
In other words, you manage what will be on your iPad by managing the representation of your Home Screen(s) on the Apps sync settings screen - almost exactly as if you were doing it directly on your iPad.Select apps to install on your iPad or drag apps to a specific screen. Drag to rearrange app icons or home screens.