Yea, subtree is my preferred choice too.
I have to manage a lot of instances with a lot of different plugins and different versions.
One of the important things to me is, you can give your customer access to the so custumized moodle repository without access to all the plugins. That's something you can't achieve with submodules.
Another thing I like on subtree is you have the whole history at one place and you can work with it without changing into the plugin direktory.