Prorating is not based on amount paid. It's based off plan value. It has always worked this way within CBSubs. We've an old feature ticket to note implementing an option for it to prorate off of paid amount instead of plan value, but there has been no progress on this for some time.

forge.joomlapolis.com/issues/7181

We have to be extremely careful about making adjustments like this. I do not know when or if this will be implemented. At this stage of CBSubs making changes to calculations could destroy businesses depending on it.

The prorating was designed this way long ago before coupons even existed (take notice that CBSubs Promotions is a plugin). So that's why it works the way it does. It has always worked this way. There are no plans to change the original behavior, but to try an extend it with an option to prorate based off paid amount, which is extremely complicated because a dozen different things can affect a baskets price.

I apologize if the parameter wasn't clear enough, but it directly states it applies to plan value. If you don't like how it's calculated I don't recommend using prorating at this time. You can try using CBSubs Promotions to apply an automatic discount when upgrading from 1 plan to another to create your own prorating behavior though. To do so I believe you'd just need the following Condition on the promotion.

To which plans this promotion applies: Plan B
Which plans must be purchased at same time: Plan B
Any of the following plans subscriptions: Plan A
Must be in state: Upgraded to other

I believe that should apply a discount to Plan B when upgrading from Plan A. Might need further adjustments to the conditions though. You could then store their previous payment amount to a CB field using CBSubs Fields and use that field as the discount amount or you could use a CB Code Field and calculate the remaining value yourself however you like and apply that as the discount.

I understand where you're coming from as well, but please keep in mind we've been in business for over 15 years. Some implementations may not make complete sense if they were implemented yesterday, but this wasn't. It was designed and implemented a very long time ago. CBSubs originally started as a means for us to collect payment to help fund CB development (which was and is still free). It wasn't even a product at that point.

With CB 3.x we hope to shed these old implementations as we shift CB into a modern stack.