By far the biggest advantage of App Sandbox is that the policy ships along with the OS. If a system framework changes what resources it accesses in a software update, Apple can update the policy so the framework functionality still works. If your app uses a custom sandbox policy, you're on your own to both notice that something has changed and to update your policy.
The downside is that the App Sandbox policy is limiting and inflexible.
I agree that there is no sense in operating dual systems, but entitlements can’t replace SBPL yet.
[1] a GUI app can restore access to files by using a trusted external selection process.
Edit: change footnote reference to prevent markup error.