I have no experience with and have heard nothing regarding using FreshBooks for recurring billing. It is my understanding, however, the FreshBooks primary focus is handling invoicing (physical and digital). This would lead me to believe that additional feature sets, such as recurring billing, would be, by default, prioritized lower for the company and therefore have a lower level of future support/expansion. Mind you this is all guess-work, but unless you're already using FreshBooks and/or interested in their invoicing solutions, they don't provide much of a draw from Braintree for recurring billing purposes in my mind.
For the record, we are currently using Chargify -- had the same issue with Braintree (Chargify does not support v2) so switched to Auth.net