Ah, this is is the biggest discussion our team is having this year. Lets see if I can show both sides of the argument:
1 Wheel-
Simpler
Gives a nice backspin on the ball
Can take up less room
Probably a slightly slower throw
Favorite of commercial ball throwers
2 Wheel-
Possibly some more velocity on the ball
With the proper setup, a side-spin or axial spin can be introduced
More complex, needs two motors or a gear/belt/chain linkage
Favorite of Physics students (Inside joke)
Now, it really comes down to which one is more accurate. You need a prototype to do this. If they're equally accurate, it depends on how much space/resources/engineering prowess you feel that you can put into it. We'll have throwers tommorrow, so we'll know then. Hopefully.

__________________
Reading makes a full man, conference a ready man, and writing an exact man.
-Sir Francis Bacon
"Any intelligent fool can make things bigger, more complex, and more violent. It takes a touch of genius -- and a lot of courage -- to move in the opposite direction."
-Albert Einstein