I don't think the power between the 2 bikes is more or less but how it's applied. Cut-n-paste 06 specs, this is why I would buy an 06.

Smooth power delivery:

First, second, and third gear torque output is key to ultimate performance, so controlling power delivery is of significant paramount. The engineers increased the crankshaft’s flywheel mass to offer greater stability on corner entry. This increased mass and the ZX-10R’s slipper clutch aid the overall effect. Acceleration out of corners is also improved as the heavier flywheel helps resist natural wheelie inclinations in first, second, and third gears.
Corner exit acceleration also benefits from the increased linear power characteristics of the new engine and its stronger mid-range performance.A new, round throttle pulley reduces throttle load and combines with revised ECU mapping to provide smoother transitional power characteristics when the rider applies gas coming out of a turn. While this feature has specific application in a racing environment, it also works when normal street riding calls for variations in throttle application.
Impressive Power-to Weight Ratio: The new ZX-10R combines the strength of its engine output, a stronger mid-range, and improved aerodynamic efficiency to deliver quicker acceleration off of turns as well as off the starting line.

More power, less weight

The NINJA ZX-10R’s liquid-cooled, DOHC 16-valve, 998cc engine benefits from new, ultra-fine atomizing injectors, as mentioned earlier.
Improved fuel atomization boosts combustion efficiency for greater power output, more linear power delivery and a smooth, step-free torque curve.
The new, lightweight Denso radiator has tightly packed cores for improved cooling.
Weight is further reduced by using a new, die-cast, one-piece seat rail.
The realignment of the engine, as mentioned earlier, provides a gain in power while reducing engine weight.