The way this is currently possible:

• Create the different versions as different modules
• Register a startup module
• Use mw.user.bucket() in the startup module, followed by a call to mw.loader.load depending on the bucketing.

I think the currently provided built-in methods for this are pretty good already nowadays:

• Module dependencies
• Extending/overwriting/overloading javascript object methods
• mw.user.bucket() (randomly bucket users according to a provided ratio and uses a cookie to remain the session)
• Extension:ClickTracking (if you it)
• Dynamic dependencies by using a javascript function as a dependency (instead of an array)

Then:

• Create the different versions as different modules (e.g. ext.fooBar.quux.v1, ext.fooBar.quux.v2; if needed they can depend on a general module that common logic, which is likely the case. You just extend it to implement the variation).
• Register an "init" module (e.g. ext.foobar.quux.init)
• Use mw.user.bucket() in the init module and call mw.loader.load to load the appropriate version.

If you want to save the additional http request, you could even go a step further and still have a common load.php cache:

• Instead of the "init" module being an in-between module, it becomes the actual module itself. With the right version as its only dependency (no scripts, no styles, no messages).
• Register the "init" module with a function as "dependencies" (in JavaScript) instead of an array. And have that return the correct modulename in an array.