Brian, it depends what the flywheels are for, on my hot air engines I use 10 32 UNF brass slotted head grub screws(ex electrical fittings), these don't damage the shaft, I use these on flywheels and pulleys. On my motors these are removed, and replaced quite often. Most of the wheels are 3/8" bore, but some of the shafts are 1/4", so the gap is taken up with a split bush, I then use a steel grub screw.
When I rebuilt a Stuart Turner S9 I used a gib head key in the flywheel, can't remember the size, it may have been 1/8", the key way cut in the shaft with a home made slot drill, the FW had the key way cut, but I had to make a new crankshaft.
An IC engine needs a very secure fixing to the shaft.
Ian S C