A microwave will heat stuff unevenly most of the time. You can get it to be better with hacks like changing the power setting and using a wet paper towel, but the evenness of heating will always be better on the stove or in the oven.
In addition, you can have more control over important variables like salt and moisture content if you don't use the microwave. Lots of food... especially meats like chicken, will dry out to hell in a microwave. By switching to a stove or oven you can rekindle the original flavor and texture.
Lastly skipping the microwave allows you to heat stuff in a more modular way. If I was reheating a pasta with grilled chicken, I would get a better result 100% of the time if I start the chicken on the stove and then add the pasta later. You get a browning effect on the chicken and you can more easily time how done it needs to be before the pasta is added.
Very good point! Microwaves are really the only way to reheat coffee. It's not as good as just finishing the cup before it gets cold in the first place, but it's miles ahead of every other option.