Yes, but there are potentially two things working against you...
1 - 29er wheels have more inertia.
2 - The pads may be new and not 100% conditioned.
Not much you can / should do about #1 other than changing wheel and or rotor size. I use Avid mechanicals with 185mm rotors, lots of stopping power. Needless to say, I'm a fan of the medium sized rotors.
In regards to #2... don't step in it
I suggest going to a steep hill and doing intervals, applying the brakes (especially front) in sudden / strong bursts (not riding them). Don't know for sure if it works, but I've heard this will help speed the conditioning of the pads.