You have several options:
Additional Plugins
Similar to how Gravity forms works, you have the base plugin which is your standard plugin, then you build additional premium plugins that integrate into it using hooks to add additional functionality
Enabling functionality
Your standard plugin bundles everything inside it, but disables sections of functionality until they’re turned on. Turning them on may be via an API key for example
The payment aspects of each solution are going to be very specific to you and how your business model is going to work, so I won’t/can’t go in to that. Personally I would recommend the plugins route