Sounds like you were on an inertia type dyno - DynoJet and Mustang are two of the more common brands. On this dyno you use the wheels to accellerate a roller of known mass, and using math derrive the torque required to achieve the measured rate of accelleration at each rpm. Then using math derrive hp from torque and rpm data.

This is better than nothing, better than tuning by ear, but as you noted really only tunes for WOT conditions at the resulting accelleration rate.

The other type of dyno is a load dyno. They apply resistance to the car via different methods and measure the actual torque the engine 'pushes back' with. Dyno Dynamics and Dyna Pak are two popular brands of this type of chassis dyno. Most engine dynos are this type as well.

They have the ability to hold the engine at a specific rpm while you operate the engine at different load/throttle openings, so that you can tune all the 'buckets' of load/vs. rpm. Imagine a graph with manifold pressure on the y axis and rpm on the x axis. Lower manifold pressure = lower load (at WOT you should approach atmospheric pressure, any thing less and you have vacuum behind the butterflys). You can then adjust the fueling with whatever method your car makes available based on the power it makes in each of those buckets, and can do the same with timing. Generally you will end up with a more driveable car with more area under the curve when tuning on a load dyno, but you get pretty close with an inertia dyno.