What it comes down to is the type of control needed.
Using Star Wars as an example, the crosshairs need to move steadily throughout the entire game screen, for it to play well.
If you use a 49-way to play it, there are only 49 distinct positions on the screen that you can place the crosshairs, and they jump from one to the next.
Using an analog, you have THOUSANDS of positions for the crosshair, and the crosshair moves smoothly between them because the distance between them is much smaller.
Road Runner, on the other hand, has Fast/Medium/Slow in any given direction.
The 49-way works well because IT has Fast/Medium/Slow in any direction as well.