I just upgraded an existing store from v0.7.2 to v2.0. It uses PayPal Payments Pro as gateway.
Now I only see credit card payments on the checkout. Currently it's all the default templates the store is using. (checkout etc.)
During testing I used all default settings and was expecting the upgrade in the live store to v2 to keep all the existing settings (where possible) when switching the live store.
I'm pretty sure the existing store (with the old implementation) had a PayPal option to pay, next to the credit cards. There are also PayPal transactions in the logs.