Yes, RB ability affects speed, not only of the RB, but any ball carrier including WR and QB and even defensive players when they intercept the ball.
You have to adjust run blocking and break block. Also, you have to be careful with defensive awareness. If that is set too high, the AI has ESP and will run to the ball even before the running back has broke through the line. For example, if awareness is set too high, the opposite side cornerback will break off his coverage and run to an angle of the ball carrier. It gets nearly impossible to break off a huge run because you'll get run down about 20 yards down the field from defenders knowing precise angles.
If you set the Break block for the defense high, and run block low, and keep awareness around 40 to 50%, you can get the defense to play the run very effectively, buty you'll get the occassional run where you still hit the hole and can turn on the jets for a long run.