I would argue that more nutrients are lost to cooking on the stove top than are lost inside a microwave.
In the microwave, things are usually covered using plastic wrap or some similar air-tight seal. Because of this, nutrients aren't able to be carried away through evaporation and steam as easily as they are on a stove top. Evaporation and steam are the only ways I can think of for anything being lost.
Microwaves work using a process called
dielectric heating, which put simply is where the molecules a piece of food is made up of rapidly rotate to align themselves to an alternating electromagnetic field which causes internal friction and heat. Imagine taking a compass and flipping it into the air as if you were flipping a coin, and what that would do to the needle inside the compass as it flipped through the air.
I'd think if anything, microwaves would work to break food down into the components it's made of and make it a tiny, though probably negligible, bit easier for the body to digest.