If you're going to base the minion limit off HD like Animate Dead, that brings up another issue with Embraced and Assimilated: The bonus HD mutation. It's not a problem with the minion cap beyond being fairly clunky, but the big problem is with the templates that can be applied to other PCs. You don't want your friends to be able to gain half their level in extra HD, because that kind of messes up the game. So, you'll want to put in a preventative clause.