In order to be compatible with Adaptive Subscriptions, a payment method must support Magento Vault for card storage. Not every payment extension supports this, including many of the PayPal payment methods included with Magento.
As noted in our user manual:
Magento Vault payment methods: The Vault adds stored card support for some default and third-party payment methods. This includes the built-in Braintree and PayPal Payments Pro payment methods. Any third-party payment method supporting Magento Vault should also be compatible. Some payment methods may require additional compatibility code to handle the rebilling process. If you use a Vault-compatible payment method, with the Vault setting enabled, customers will be able to purchase subscriptions using that payment method. Be aware that the Magento Vault does not provide the ability to add or update credit cards outside of checkout. Also note: Adaptive Subscriptions supports $0 checkout, but not all payment methods do. Of the payment methods listed above, Braintree does not support $0 checkout. Third-party payment methods may or may not.
Additionally, while Braintree offers a PayPal solution, in the latest versions of their payment extension they do not support using the Magento Vault for guest checkout. To avoid issues, we recommend requiring an account to checkout when using Braintree's methods with Adaptive Subscriptions, or looking into a third party credit card or PayPal solution that fully supports Magento Vault for checkout.
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