I think the biggest advantage of a micro-controller (like Arduino or an MSP) or prototyping microcomputer (like the Pi or BeagleBone) are control of GPIOs from

I think the biggest advantage of a micro-controller (like Arduino or an MSP) or prototyping microcomputer (like the Pi or BeagleBone) are control of GPIOs from a reasonably high-level language. At least for my applications. serial and parallel ports on PCs used to give you some functionality similar to this too. But smartphones lack that for the most part (the best you can expect is typically bluetooth comms with a separate device). If you need remote logging, the 3G Particle Electron boards (particle.io) should be released soon, which I'm pretty excited for.