Possibly. But what would he have to do in the real world to get abilities in the Matrix? If Neo and Smith-in-someones-body were on beds in the Matrix, and Smith 'assimilated' him or something, maybe, but what does one do on the outside world do get those powers into the Matrix? And the body Smith inhabits in the world would still have to be jacked back into the Matrix, if he wanted to use those powers inside the Matrix.
Also, Smith has always had these powers of speed/agility/etc because he WAS an Agent; he just lost the Agent purpose, but not Agent abilities. And he could have had a small upgarde when Neo jumped in him, assuming some of Neo's code of ability also got written to Smith.
May sprout into a good idea. Expand on it though