It doesn't make sense for Ebay to own 2 Paypals. The reason they bought Braintree in the first place is to extend their reach into a different market. Braintree customers chose Braintree because it is NOT Paypal. If I was you I wouldn't be worried too much. Just keep watching the quality of service you get from Braintree and if it starts going down too much, then change.
A blog from the founder and CEO of Braintree Bill Ready explains that they will continue to work independently whilst adding value to PayPal's weak points; customer service and the younger consumer generation of customers. https://www.braintreepayments.com/blog/braintree-teaming-up-...
At Braintree we have always earned our merchants' business every day. We were the first payment platform to offer data portability, because we don't believe in locking in our customers, and that doesn't change. As we enter this new chapter, will we continue to earn your business with same great support you've come to expect and even more of the innovative technology you've come to love. Our support and accounts teams are still just a call (or email) away: 877.434.2894 or support@braintreepayments.com.