Stir together cream cheese, vanilla extract, and 1/2 cup sugar in a medium bowl. Set aside.
Combine 1/2 cup sugar, 1/3 cup flour, and 1 teaspoon cinnamon in a small bowl; cut in butter with a fork or pastry blender until large crumbs form. Set aside.
Combine remaining 3 cups flour, remaining 1 3/4 cups sugar, remaining 2 teaspoons cinnamon, cloves, and next 3 ingredients in a large bowl.
Whisk together eggs, pumpkin, oil, and milk in a medium bowl; stir egg mixture into flour mixture just until moist. (Do not overmix.)
Spoon half of batter into prepared muffin pans. Dollop about 1 tablespoon reserved cream cheese mixture in center of batter, and top evenly with remaining batter.