The Web Services API is implemented as a layer on top of the Foundation Services API, so it doesn't really make sense to compare them directly.
It's best to think of the Foundation Services API as being Alfresco - everything else (Web Services, Web Scripts, JCR, Javascript API, PHP API, WebDAV, CIFS, FTP, NFS, Web Client UI, etc. etc.) are simply layers on top of "native Alfresco" (the Foundation Services API). Capabilities such as clustering are built into the repository (ie. into the Foundation Services API), so it doesn't really matter which access mechanism you use - they all behave much the same when it comes to this (and other) capabilities.
What's more relevant is how you wish your users and/or other systems to access Alfresco - that's the single biggest factor in determining which of the various access mechanisms is most appropriate.
Cheers,
Peter
