Peaceful co-existance between iPads

I received an iPad mini for Christmas. My wife already had an iPad 2. Her iPad was set up to synch with my iMac. I have also logged my iMac into her iCloud so we share common pictures, apps, etc. The iTunes account on my iMac is signed into my apple id. She has loaded her own apps as well as some of my apps onto her iPad. When I got my mini, I put it under my iCloud account and originally synched it to my iMac. I loaded several new apps using my Apple ID. My intention has been to separate the 2 iPads, removing apps she had loaded under her ID and adding copies of my own. That way, when the app store icon pops up saying there is a new version, I do not have to enter her apple id as well as my own. When synching iPads, I have only selected the apps she wants on hers- and I have done the same with mine.

Here is the issue- she keeps getting the new apps that I have loaded on my Mini, onto her iPad. She has her iPad set up the way she likes it- does not want new apps unless she loads them. That is understandable, as I want the same with my iPad. Can I keep the 2 separate, but still synching to one iMac? Is there a setting I am overlooking that I need to have to avoid sharing apps between iPads (unless we want to)?

Thanks in advance for any suggestions.

Mark