You are going to invent a new device that people can use instead of a microwave to warm up leftovers.

OK.  I would build it the same shape and size as a microwave oven, but I would leave out all the normal electronics.

In the side compartment, in place of the electronics, at the top, I would put a little gas flame, like a Bunsen burner.  In the bottom of the side compartment, I would put a treadmill with two strong hamsters.  Then, I would install ductwork in the compartment so that when the hamsters turn the wheel, some fan-blades along the rim of the wheel would blow the hot air from the gas flame down and into the big food compartment.  This would warm the left-overs WITHOUT using electricity from the wall outlet, and without spraying any hazardous high-power RF energy into the kitchen.  

what experimental evidence led scientists to change from the previous model to this one?

a few of the positive particles aimed at a gold foil seemed to bounce back.

the colors of light emitted from heated atoms had very specific energies.

experiments with water vapor showed that elements combine in specific proportions.

cathode rays were bent in the same way whenever a magnet was brought near them.