The likelihood of another species of hominidae, rivaling our intelligence anytime soon, I'd say is slim. Evolutionary changes typically take place over very long periods of time. While short bursts of mutations are possible, we humans would probably have a pretty firm grasp as the dominate ape species.
The matrix scenario, while wild, I would guess is far more likely. Our computing power continues to grow at a pace that would almost undoubtedly reach that point before another species could ever compete with us. I read in a time article that we could be in a "computers building computers" scenario in less than 50 years. Do I believe this? I'm skeptical....
But if I was in a casino and told I HAD to bet on the two... I'd definitely put my money on the matrix scenario first. Although I don't know it would be as grim as the Matrix... And obviously I'm assuming a far more practical version of each story. Super computers / robots likely wouldn't use us for "batteries" because we would need to be fed... Which would require enormous amounts of food and just be more inefficient than just killing us in the first place.
All of the is speculative... I didn't even cite anything so don't take this post too seriously :) Train your brain to be skeptical :)