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You didn’t mention anything about the implementations you’re using so it’s hard to say anything about them 🙂
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I don’t know if your benchmark is representative of anything, I’m not sure it allows to make any valid conclusion.
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JAX-WS is supposed to perform better in general than JAX-RPC, see the already mentioned article.
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JAX-RPC is a dead standard that has been pruned in Java EE 6 (and might thus be removed from future versions). Reason for Pruning: JAX-RPC was an early attempt at modeling SOAP web services as RPC calls. Web services have since grown out of being an RPC model. The much more robust, feature-rich and popular JAX-WS API effectively supercedes JAX-RPC.
To summarize, I would definitely not base a new project on JAX-RPC.