If you have both a scope and a logic analyzer available, and want to just look at the protocol level, then clearly a logic analyzer, or even a protocol analyzer like the TotalPhase devices (I have one I got really cheaply), would be the superior choice. But in a pinch, or if you don't have a logic analyzer available, I could certainly see using a scope for protocol decoding.
And of course where you need mixed signal ability of say the SPI input to a DAC and the analog output from the DAC, but probably not on a 2-channel scope
