Check out the newest issue (March 2010) of Diesel Power Magazine for more information about the Pros and Cons of the Allison Auto from 2001-2010.
According to DP the Allison has the following weaknesses:
ADAPTIVE LEARNING - The Allison's learning curve. You've heard it before and know that it's what makes the Alli' great for stock trucks, but not so amazing on modifed trucks.
C3 Clutch: Suffer from lack of lubrication. The only time the clutch receives fluid is when it is applied.
C1 and C2 Clutches: (5SPD Only): The apply pistons that engage these clutches are off-centered, leading to uneven pressure being applied. When they are worn, they are only 50% worn.
DP also states that if you want your factory Alli' to last you shouldn't juice your DMAX more than 90HP on a 5SPD and no more than 120HP on the 6SPD.