Definately refinish the hardwood floors. Paint the walls something other than white. Paint the doors at the bottom of the fireplace a dark gray to make them blend with the stone. I think (based on the picture) that there isn't enough room for bookshelves next to the fireplace. Pictures from different angles would be helpful along with pictures of the desk, chairs, lamps, rugs, art, etc. that you plan to use. I would like to see Groveraxle help with your project. His/her advice is amazing.

I'm not fond of the flooring with the stone as the flooring is too busy. A rug would help.

I would get rid of the stone fireplace. Drywall and do a simple stone facing. Get rid of the hearth. The simpler you make the fireplace the better. Are you tearing up floors and replacing with wood?