This is a puzzler! Very rugged looking fireplace although many of the rock are quite nice. Are the shelves back rather far from the edge of fireplace? Almost looks as if you would have to stand up on it to arrange or clean shelves.

Maybe they should just be dry walled in and call it a day! The colors you picked for the kitchen are quite nice. You are having two different cab. colors?

Is the ceiling pine? If so, I would either stain it darker or paint it. What color, I do not know. Good luck and I will check back.

A lot depends on what feel you want to achieve in your home. If you want country cabin then I would leave the ceiling, build more shelving to the ceiling and over the door and paint all walls and shelving the same as your first photo of your kitchen. If you want modern I would pull out the shelving and dry wall. I would then paint the walls grey white and the ceiling a grey write wash. Your kitchen would then need to be more contemporary in a white.

I think the issue is that the lines of the left big shelves, the small shelves, the mantel and the other small shelves don't visually line up at all. I don't know if the shelves are at all adjustable (which might be a good retrofit if you can do it), but I would try to get a more linear thing going. I'd take out the "drawer" piece, and use that area for stacked logs as you see in so many photos. If your contractor could beef up the mantel by about 2x at least, I think that would improve the ratio of the heft of stone vs mantel. I'm not usually a fan of gray (whoo, odd!), but painting the built ins a stone gray, or black like your other cabinets, leaving the mantel wood as the ceiling color, seems the way to go. I actually really like the wood ceiling. Seems like it ties in the colors you show as the countertop.

I don't mind the fireplace stone or ceiling, except for the front ledge in front, but that would probably be a big undertaking to remove. The mantle needs to be chunkier. Align shelves as nwduck suggested, and paint them a med gray.