I've experimented with using Custom Actions in lieu of Custom Commands and in a handful of tests, they seem to do everything for which I've previously used Custom Commands. Under RM3, when would I want to create a Custom Command?
IHMO, Custom Actions are similar to a private boolean, perfect for interacting with a single rule. Custom Commands are like a Global Variable, they can be used with many different rules.
If you only need to use the command in a single rule, custom actions are the way to go, if you need to use it in multiple rules custom commands make it easier.