As far as I know, vSphere Replication does have several limitations comparing with Veeam B&R. Few that crosses my mind:
• vSphere Replication provides single restore point only. It can be considered as a limitation number 1.
• Lack of failback functionality.
• No traffic compression.
• No traffic throttling.
• No network customization (network mapping).
• No re-IP upon failover.
• Basic VSS quiescing (no application-aware processing, which is necessary for replicating VM running VSS-aware applications (such as Active Directory, Microsoft SQL, Microsoft Exchange, SharePoint), since this functionality guarantees backup transactional consistency of such VMs).
• Works within single vCenter only.
Hope this helps.
Thanks.