Some research say that M/W cooking actually help to retain some of the vital nutrients in cooking which is otherwise lost in other methods. But to ensure that the nutrients are not being sapped proper technique has to be ensured while using M/W

1. Make sure to arrange your food uniformly to prevent uneven cooking.
2. Cooking for minimal periods is essential since too much cooking time can sap out nutrition - which is why arranging uniformly is essential.
3. Minimal water has to be used. If using frozen vegetable, no additional water is required since the food will cook in its own juices. Otherwise add few tbsp of water -i.e as little as possible.
4. Cover and cook. It could be lid that comes with your M/W utensil or it could be a vented plastic wrap. What this does is, it creates steam which is responsible for destroying bacteria and also helps to cook the food uniformly. I have heard of Oven cooking bags which are good for this although I have not personally used them.
5. At times, its inevitable that there is uneven cooking in m/w however uniformly you arrange your food. Hence it is important to stir/rotate your food in the middle of cooking for the food items which are in the "cold spot" where chances of bacteria retention can be high. This tossing and stirring of the food in the middle of cooking helps.

Having said that, I personally do not use Microwave for my cooking. I find cooking in them more cumbersome than stove top cooking.