Currently there's two checkboxes in the publisher options:
Copy the assignments from previously created applications or updates when an updated application is created
Delete the assignments from previously created applications or updates when an updated application is created
I suggest splitting this into four controls to manage applications and their updates separately like so:
Copy the assignments from previously created applications when an updated application is created
Copy the assignments from previously created updates when an updated application is created
Delete the assignments from previously created applications when an updated application is created
Delete the assignments from previously created updates when an updated application is created
My current update assignment schedule is pretty long, with the last batch getting updates 2 weeks after publishing. This means when an app is updated more than once every 2 weeks, the latest version will never hit those machines since the assignment for version n-1 to that batch gets deleted before it's available.
Since I'm also publishing the applications to all users, the "copy the assignments" function will result in all users having two versions of the same app available to them.
It would be handy to set these options separately for apps vs updates, allowing two updates to be published simultaneously while only one app installation is available.