The only time you should prefer the use of SOAP over REST is when REST is incapable of handling the integration, or the third-party system does not support REST.
In your example scenario, you can use SObject Get Updated and Retrieve Multiple Records with Fewer Round-Trips more efficiently than getUpdated*( and retrieve().
At this point, there are very few, if any, SOAP calls that you can't do in REST, so the primary concern for most cases is whether your environment supports REST or SOAP better.
REST has many benefits, primarily reduced bandwidth and memory usage (in typical environments), and ease of use in supported languages. The only benefit that SOAP had over REST is that IDEs could auto-complete code without the help of a library, but since REST is so easy to use in most environments, that's hardly any benefit at all.