A floorplan with measurements would help.

If you get a larger rug, perhaps you can run electrical under it for a lighting. Or see if it would be too expensive to add some flush floor outlets.

It looks like the best spot in the room belongs to the cat (and the cat looks peeved in the one photo without the cat tree). I guess we want our cats happy because they make us pay for it if they aren't, but does the little table fit in that area? It might be a nice place for games/homework, cat permitting, of course.

It's a great room with lots of interesting aspects. Those are the worst to set up. :)

I think book case looks good there, going well with all wood. Just declutter it and decorate better. Console with wall art above and lamps is a good idea.

I'd put the TV on a swivel, and move the sofa to that solid wall.

Buy a few more pieces of upholstered furniture (a couple club chairs,)

Move the glass table to the window area w/ chairs. ... looks like you even have room for a sofa under the stair rail/kitchen seating wall. since you are updating the railing, I;d paint out the storage/kireplace shelving and that odd wood slope on the wall(s). Even a much larger area rug with some color/interest.

I think the fireplace has a lot going on and is definitely the focal point of the room. If you don’t need storage I would remove the cabinet - it is a clutter magnet. I would not add shelves to the fireplace as they would attract clutter, too. I might put a great floor lamp in that corner and a big snuggly chair to hide the electrical outlet. It’s a wonderful room with all that light. Simplicity is what I would keep in mind going forward. Will you be purchasing four chairs for the glass table?

I would paint the fireplace and wall unit if you want to keep it - all the same color. SW Urbane Bronze comes to mind - def not white. Maybe there is a warm charcoal color that would work, but your floors are very warm, so you have to be sure not to use a cool color. IMO there is nothing to be gained by replacing the wall unit with floating shelves. If you have children an enclosed wall unit might be your best bet, but still with everything on that wall the same color. Or remove the existing wall unit and leave that section of wall blank as another poster suggested. What is under this room? If the joists are open underneath you could add floor outlets.

What if the mantel is dark, the bookcase is dark, all the shelves removed and you create a collage. This idea:

Nice big chair and lamp to replace built-in.

Thanks for the comments, everyone. I should have explained that the bookcase is not usually that cluttered! :) Appreciate all the feedback.

Since you mention clutter, and a houzzer mentioned good idea of hiding clutter with doors - do you like the idea?

Kitty might be saying, "I'd like a bed where the lower doors are... why not?" ;)

Which photo shows the room as it is currently?