I don't believe there is proper space for shutters, but I would definitely paint all the window frames dark. That white sticks out like a sore thumb.

I think I would invest money in some spectacular landscaping and trees to take the attention off the house and break up the big expanse of HOUSE.

If you paint the stone, it will look like even more of an eyesore.

Instead paint the window frames dark as others have suggested and for the stucco pick up one of the stone colors and paint it the stone color so it doesn't stick out as much.

The "rock" is already grey! And it's not rock, it's stone.

You're buying a McMansion; with faux stucco and cheap rectangular windows put in arched openings that are infilled with glass above. Don't make it worse than it already is by painting the stone.