I have no direct answer on how to solve the problem using Gradle, but I have a suggestion that can help you increase the speed of your collections.
I recently ran into the same problem: our assembly took about 4 minutes. I tried different build options, but did not get any noticeable profit.
After some research, I came across Jrebel for Android . This is something like "Instant run" on steroids. It supports many types of changes (user interface, methods, fields, etc.) and updates the application in real time without repeated activity (therefore, saving state). It usually takes ten thirty seconds to apply any changes.
The tool is not free, but they provide different pricing options and a trial account, so you can try it. It works like a regular plugin for Android Studio or Eclipse, and the installation is very simple.
Update
Now they even have a free version: link for publication
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