Preheat oven to 375°F Let pie crust stand according to package directions.
In a 12-inch skillet heat butter over medium heat; add onion, leek, shallots, sugar, nutmeg, pepper, and 3/4 teaspoons salt. Cook about 8 minutes or until tender but not browned, stirring occasionally.
Reduce heat. Stir in cream cheese until melted.
Stir in Swiss and Monterey Jack cheeses until combined.
In a large bowl combine eggs and cream. Gradually stir in onion mixture until combined.
Ease pie crust into 9-inch pie plate; pour onion mixture into pie crust. Fold edge of crust over filling, pleating as necessary.
Bake, uncovered, about 40 minutes or until crust and top are golden brown and a knife inserted near center comes out clean.
Cool on a wire rack for 15 to 20 minutes. Cut in 16 wedges. Serve warm.