Something on Discovery Science last month just happened to nicely combine these techs, but with electrodes stimulating brainwaves instead of reading them: A New York team of scientists, have worked out a process where 3 hair-thin electrodes are inserted into a rat's brain, one to each area of whisker nerve endings and one to the pleasure center of the rat's brain.
The electrodes lead to a battery pack radio combo backpack, light and snug enough to not interfere with the rat's movement, stimulating either whisker cluster feels like a touch on the end of it. If they turn in the direction of the touch they get a 'good feeling reward' and can easily be directed by a human.
I've seen footage, they work and they plan to use them in rescue operations where quarters are two cramped for dogs (which still have a great advantage in scenting trapped people), though there's still discussion in how biological rats compare to more heat resistant robots.
If you want my two bits: The electrodes to the nerves don't seem to me to be a form of 'mind control' or brainwashing, as the rat has a choice over whether to turn or not, on roughly the same principle as a trained dog responding to signals, but that pleasure center thing sounds pretty addictive...
Here's an article on the experiments from back in 2002 when they had only five working rats: http://www.wireheading.com/roborats/ratbot.html Trust me, they've come a lot farther since then... I'd like to see this tech applied to those mine sensing dolphins.

Now, think about a post-modern Shadowrun with these guys as rigging toys, I don't see any reason that by 2060 this won't be applicable to all trainable animals, our main limitations right now is our understanding of brains and our lack of finesse. If 'unethical corps' actually used this tech to get previously untrainable paracritters addicted... Or their wageslaves.
As far as bio-rejection issues go, what do you think the expected Essence cost of radio nanites to be, 0.1?

Yeah, I can just picture a drone rigger and an animal rigger sitting down and arguing over customizable drones versus dual-natured critters...