Payment Gateway
One of the most important limitations set by Shopify is that it currently requires all merchants looking to install any subscription app to use one of the below payment gateways.

However, Shopify is enhancing their payment gateway support, and has planned to include other payment gateways by the end of this quarter. You can find more details on Shopify's payment gateway support roadmap here:
​https://shopify.dev/concepts/apps/subscription-apps#product-roadmap

Draft Orders (or manually created orders):

Shopify currently does not support adding a new and separate orders within an on-going subscription. A merchant can add or swap products in a subscription, and also skip a scheduled delivery. but he/she cannot manually insert a new order.

Accelerated or express checkouts:

Accelerated or express checkout helps returning customers to checkout quickly by using their pre-saved billing and shipping information.

The limitation to use the accelerated or express checkout features comes directly from limitation No. 1 (around the payment gateway). Since accelerated checkouts are usually with third-party gateways such as Apple Pay, Google Pay etc, and as Shopify currently limits subscriptions to Shopify Payments, Stripe, Shop Pay and PayPal Gateway, the accelerated checkout feature for other payment gateways cannot work with any subscription application right now.

Shipping Rates:

Currently, Shopify, by default, shows your customers who subscribe for recurring orders only the cheapest shipping plan within your store, and does not provide multiple shipping options. This is to save shipping costs for the merchant (and customer) on orders that are placed well in advance - the recurring orders.

Shopify Buy Button:

A buy button is a shortcut that leads to the checkout process. It basically allows the merchant to embed their product/service card in other non-Shopify websites or blogs, such as Wix.com. Currently, Shopify does not allow any subscription apps to integrate with the Shopify Buy Button.