It's been done, especially in larger scales, BlueRail, Dead rail society, CVP Airwire and more, the new Soundtraxx Bluenami decoders allow direct control of a model equipped with just such a decoder by iPhone or Android Smartphone.
The Bluenami with the direct Bluetooth link from the model to the phone would be the perfect candidate for dead rail with a battery pack for power. It's the newest form of direct communication from controller to locomotive model.
I am researching this myself right this moment, trying to find batteries that would be small enough to fit in HO scale equipment, yet with enough power to run the models steady for at least 4 hours at a time. The 14.8 volt R/C car batteries look promising.
With diesel locomotive models the batteries could be housed in a second "dummy" unit which would look fine anyway as a multiple unit lash up on trains, for steam locomotive models, the batteries would need to fit in the tender, or in a boxcar behind the locomotive.