A standard electric stove can have 2500W elements, and most of this energy will go into a kettle sitting on the element and thus heat the water. Even a big built-in microwave won't consume much more than 1000W, and a fair percentage of that is wasted in heating the magnetron (I've found citations of 50% to 70% efficiency). So, all else being equal, a kettle on a stove will heat a body of water 2-4 times as fast as a microwave oven.

With a mug of water the convenience will likely outweigh the lost time, but if you're heating a liter or more of water then you probably want to pull out that kettle.