a shorter pin with allow the ball to roll up a little quicker than a longer pin. the longer pin will be more skid/flip while a medium pin will allow the driller more versitility when setting up the ball to do what you desire.
--------------------
300 x 5   800 x 1
check my ebay auctions here.
http://search.ebay.com/_W0QQsassZ61lesiaQQhtZ-1
Proud new owner of lane #1
Tsunami
Cobalt Bomb
Black Cherry Bomb X2
X L PRO PURPLE  
Gold Nugget
Enriched Uranium
Army Carbide Bomb
Uranium HRG X2
And the almighty

              G-Force

Additionally, pin distance might limit drilling options. If you have high revs, a short pin will force the ball driller to put the pin under the fingers to keep the CG in legal limits, and this might result in flare across the finger holes on the back end, if the ball has a high differential.
Basically, a short pin makes sense when you want a rolly ball and an arcing setup. The longer the pin, the more potential for a flippy reaction setup is given. But that's quite rough, static weights might also play a role.
--------------------
DizzyFugu - Reporting from Germany
Doing legwork on bowling? Check out BR.com's vault of wisdom: the unofficial FAQ section