How to perform product version controlling for WordPress plugins

We have a stand alone application dealing with

1. CRM (Customer Relation Management)
2. CFM (Cash Flow Management)

In our stand alone application we have three pricing modules for the product categorized in to three types

1. Standard
2. Advance
3. Enterprise

Each having different pricing, functionality limitations and Options

Recently we have decided to develop our WordPress plugin so that WordPress users can also integrate their e commerce or other sites with our platform and manage their data easily

The issue we are facing is that how can we manage the WordPress version controlling with it

there are two ways to do so (that i think of)

1. develop a standard plugin having all functionalities in it and enable functionalities based on user package e.g(if our user has subscribed to ADVANCE version of our application, we will enable all the functionalities related to it and disable all other functionalities related to Enterprise version)

2. second way is to upload three versions of our plugin on WordPress market each having functionalities related to their version (Standard,Advanced,Enterprise)

if we go with the first method the plugin will be easier to manage in future as there will be only one copy of the version which will be updated but there is also an issue that user can easily edit the code of the plugin and bypass the functionality limitations and can use Enterprise version of the plugin by being the member of Standard version

On the other hand if we go with the other method that is creating three versions of the plugins it will be hectic to manage the code of the plugins as any amendments in future will result in doing the same work three times

how can we overcome this problem? what is the ideal way to manage these type of situations