The main value is central customer and subscription database, which muxes multiple payment methods: Credit Card (via Stripe), Amazon payments, and Paypal. This alone has doubled our monthly paying customer growth.
Next it allows us to create invoices, subscriptions and customers data to put in the same database for customers from other channels -- mostly this is our iOS users who have to subscribe via iTunes (due to Apple TOS) -- now we can manage their data in the same place.
It is also an integrated coupon management system, hosts custom styled payment/subscription management pages (as opposed to just a tiny payment widget like Stripe), supports more flexibility like trial periods, switching between subscription plans, adding credits to a user's account.
We've moved all our non-iOS customers to Chargebee for about 6 months now, and really happy with it.
I moved from Chargify to Stripe about a year ago (to save on cost) and the biggest challenge was getting customers to re-enter their card details for Stripe.
I offered a coupon for 50% off a month's subscription to entice them to do so but still resulted in a couple of months of paying both Chargify and Stripe while I chased the errant customers.
I can't give numbers for our ROI, but we spend far less time providing payment/subscription support, and pay a flat extra cost to Chargebee for the added abstraction layer they provide so it's easy to evaluate -- worth roughly 100 subscribers/month, and since shifting to Chargebee we gained more than that number within the first month beyond our regular month/month growth.