For example, I personally don't like prorating costs. I want my customers to be able to make changes and play around with the new features before deciding to pay. I also don't like the idea of having a few plans and forcing every single customer into one of them. I want everyone to use the software how they want, and pay based on that usage. These are important business decisions that would be impossible (or at least very difficult) if I used a pre-made subscription system.
Luckily Stripe makes it incredibly easy to roll your own subscription system.