I found the science of this questions on another forum...
But from personal experience - Large High performance brakes (cross drilled and same weight as oem), Larger wheels (same weight) and any other components (you wouldn't put a larger diameter flywheel on - but if you could) - they ALL increase the rotational mass necessary for your car to overcome at acceleration. It's simple physics.
The power to accelerate a rotating system is given by P = (torque)*(da/dt) where a is angular position and t is time. Torque is equal to the product of the system's rotational inertia (I) and the system's angular acceleration (dw/dt) therefore this can be rewritten as
P = (I)*(dw/dt)*(da/dt)
Thinking of the brake/tire/disk system as being one solid disk and, since the rotational inertia of a solid disk is given by
1/2(M*R^2) (where M = mass and R = radius) this can be rewritten as
P = [1/2*(M*R^2)*(dw/dt)*(da/dt)] = 0.50(M*R^2)*(dw/dt)*(da/dt)
If the mass of the disk is reduced by, for example, 25% but its radius is increased by 20%, the power to accelerate the new system would be given by
P = [1/2*(0.75M)*(1.2R)^2*(dw/dt)*(da/dt) = 0.54(M*R^2)*(dw/dt)*(da/dt).
An engine will have P flywheel hp available to accelerate the brake/tire/disk system, therefore (at the same rpm)
0.50(M*R^2)*(dw/dt)*(da/dt) = 0.54(M*R^2)*(dw/dt)*(da/dt).
For a given rpm, da/dt are equal on both sides of the equation therefore
0.50(dw/dt) = 0.54(dw/t), dw/dt = (0.50/0.54)*(dw/dt) = 0.93 (dw/dt).
That is, for the flywheel power available at any given rpm, the brake/tire/disk system with the reduced mass but increased radius will have an acceleration of only about 0.93 that of the unmodified system.
The dyno roller which is accelerated by the car's tire has its own rotational inertia (I) and the power it measures is given by P = (I)*(dw/dt)*(da/dt). Since for a given rpm, its I and da/dt are the same, it will measure a lower hp reading from the lower acceleration of the modified brake/tire/disk system, i.e.,
P(1) = (I)*(dw/dt)*(da/dt) > P(2) = (I)*(0.93*dw/dt)*(da/dt).