Melt the 1/4 cup butter and sautee the onions in it until soft. Sprinkle the flour over the mixture. Cook and stir over medium heat for 1-2 minutes.
Whisk in the half & half and chicken stock.
Add the broccoli and carrots. Cook over low heat for 20-25 minutes or until the broccoli and carrots are tender.
Add salt and pepper. You can leave the soup chunky or blend about 1 cup of the soup and stir it in for a smoother soup (that's what I do). Return to low heat and add the cheese. If your heat is too high your soup can get grainy. Stir in the nutmeg if desired.
Serve with crusty bread.