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 be rated at much more than 1000W, and a fair percentage of that is wasted in heating the magnetron (I've found citations of 30% to 50% wasted power). 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.
Edit: if you're talking about electric kettles, then in the US (120VAC) they're 1000W to 1750W with very high efficiency, so they'll still be faster than anything but a commercial microwave. In the lands with 220VAC power, kettles can be up to 3000W, which would be even faster than a stove-top kettle.