The verdict
For most small B2B software teams, I'd pick Stripe by default. It is the safest first choice, because most tools in your stack already integrate with it, and you keep control of checkout, customers and data. If you sell digital products worldwide, have no one to run tax and compliance, and would rather hand that over, I'd pick Paddle.
Stripe needs a developer for anything custom, and its billing, tax and reporting add-ons are priced separately. Paddle means customers see its name on their statements, and it reviews your account. Whichever you start with, ask how subscriptions and stored payment methods can migrate if you switch.