The first bike I made went through the crank. I hated it. It was a lot harder to gear the motor to the crank speed. I also did not like the crank sprocket spinning while I wasn't pedaling.
With my current set up I can adjust the motor gearing and the pedal gearing independently and therefore It is much easier to make them match. It would be nice to have several gears for both the motor and the pedals though. I only have a single speed for the pedals. If I pedal and do not use the motor, then both chains from the rear wheel turn, but you do not feel much drag. I could set up a single speed for both the pedals and the motor and then only one chain would move if I was only pedaling or only using the motor.
If you went with a internal geared hub, then you could have 3 speeds for both, but they would be tied together. You would also want a slipper clutch on the motor drive somewhere to stop from munching the IGH.
Lastly, if you eliminate the freewheel crank, then all the problems of it disappear as well. You can use any bottom bracket that gives enough clearance and you do not have to worry about overrunning a freewheel.
I often pedal with the motor, but only when on the bike paths and at lower speeds. I have a lyen 3 speed electric switch and run at about 60% (I think) power on the paths. Then the pedals and the motor match very well. I can also pedal without the motor fairly easily, just not up hill. If I run full power, then I can only pedal up to about 20kph, then I can't keep up. I could easily change the gearing to suit that speed, but then I could not pedal without power. In full power, my top speed is 50kph.
Hope that answers your questions.
Clay