I can see how the ability to exclude some apps from updating could be useful:

In my case I have one particular app installed that I like quite a bit in its current state, and have not encountered any bugs in my usage. Meanwhile, the developer of this app is currently undertaking some dramatic re-writes to the UI that I'm not particularly fond of (absolutely their prerogative to do so), and as a result I have no interest in updating at this point and losing the version of the app that I like.

However, I'm also using a number of other apps which are in need of updates from time to time, so I have no interest in disabling the Extras repos or the automatic update checks since I find that feature useful..

IMO it would be great to be able to simply long-press an app and tell App Manager to ignore updates. An item called "reset ignored updates" could be added to the App Manager menu.