I haven't worked with the PayPal API extensively, but Stripe does a lot of customer management, subscription management, itemized invoicing, etc built-in, which I don't think PayPal supports.
Personally, I think any difference in price pays for itself in developer time, unless you have billions of dollars in yearly revenue. The PayPal API always makes me want to gouge my eyes out, whereas the Stripe API is so pleasing to use that I'm looking for reasons to integrate Stripe into things.
You don't need billions in revenue to recoup the cost of a few extra developer hours. Pay pals new REST API doesn't even look that hard to use, either (I've only used their older APIs)
Personally, I think any difference in price pays for itself in developer time, unless you have billions of dollars in yearly revenue. The PayPal API always makes me want to gouge my eyes out, whereas the Stripe API is so pleasing to use that I'm looking for reasons to integrate Stripe into things.