You should post your question at the home decorating forum. Lots of people will provide suggestions on layout, etc.

Build or buy shelves that go UP UP UP. I live in NYC, and we know that when you can't spread out, you have to go up.

Save your bookshelf money until you can get shelves that are very tall; don't squander it on something "just for now."

Go for back-of-the-door storage w/ shoe pockets; and put shoe pockets on walls, on the sides of bookcases.

The Command strips are your friend; you can use them to stick all kinds of stuff to the wall, as long as the stuff has a flat back (I've taken the plastic cups that are sold w/ suction cups to go in the shower, removed the suction cups, and stuck them to the inside of the kitchen cabinets, or the wall next to the sink for toothbrush & toothpaste.)

You've got some decent closets there! That should help.

In your walk-in closet, get something like milk crates or wooden cubes to go around the edge under the clothes; that will create two levels of storage.
In fact, you might pick something that's going to be around a while, and buy add-ons every now and then.

BATHROOM:

In apartments, you often can't make holes, etc.

So, for the shower:

tension-rod shower towers are often good:

Put a tension shower-curtain rod across the back of the tub, sort of high up, and use S hooks to hang handled baskets; that creates a place to stick your shampoo.

Try to figure out what you want to do in each room before you do anything else.

Kitchen could be: cooking, making coffee, baking, eating, meal planning.

Living room could be: tv watching, video games, board games, reading, visiting with friends, place for a guest to sleep, home office space, sitting and doing nothing, surfing on tablet/laptop, working from home, listening to music, snacking, drinking.

Bedroom could be: sleeping, getting dressed/undressed, tv watching, net surfing, home office space, reading in bed.

Most homes these days need a charging station. Where will you put yours?

Do you have any hobbies? Where will you do these and what equipment will you need?

Do you have or want any exercise equipment? Even yoga needs a place to stretch out, and a place to store a yoga mat.

I would also look into make a little space for a "launching pad," a place where you can easily store and retrieve the little things you use every day--keys, phone, wallet, briefcase, etc. This is usually located near the front door. In your apartment, you might be able to put a small table or bookcase on that short wall directly across from the entry. Use a small bowl or tray for keys. If there's an outlet there, you could set up a charging station. Your bag could go on a shelf or under the table. So you walk in, drop off keys and phone and bag, and if that's a closet in the living room right next to that wall, hang up your coat. Easy, and then all that stuff doesn't get strewn all over the place, and you can find it easily the next morning.

Once you have figured out what you want to be able to do in a room, then figure out if you have the right supports to do it.

For example, you want a home office. Do you have a table or desk, computer, filing/storage for papers, basic office supplies like stapler, paper clips, pens, pencils and a place to store them? Good lighting? A comfortable desk chair? (Which could also serve as guest seating if necessary.)

You want to read in the living room. Do you have a comfortable chair? A side table to hold books, coffee mug/wine glass, good lighting, a footrest if you like one?

You want to host weekly Monday night football game TV watching parties. Do you have enough seating for all your friends in locations where they will be able to see the screen, places for them to safely put down food and drinks, enough glasses/serving pieces to hold the food (or just room in the kitchen cabinets for enough paper plates and cups).

Your brother will be coming to town every month or so for the weekend. Do you have a place for him to sleep (air mattress, sofa bed), a place for his luggage, space for his stuff in the bathroom (place to hang his towels, etc.)?

Based on what you have for the living room, I'd say the first things you should look into getting would be a) storage of some sort--bookcases or a credenza, b) one or more comfy chairs for guests, and c) a coffee table or side tables to hold drinks, remotes, laptop/tablet/phone, snacks, etc., and, depending on the lighting situation in your apartment, d) lamps--many people do not have enough light in their apartments and need a mix of floor and table lamps.

Living-
I don't know what kind of tv unit you already have, but I recommend everything you buy to also be something you can use for storage. I used to have a tv unit that was just a couple shelves so I couldn't put a lot on it in terms of storage without it getting cluttered. Now I have a unit with three separate cupboard doors so that I can hide many things away like dvds, chords, and whatever else. Some units even come with drawers which can be super handy for this also.
I like to use this same thinking for most of my pieces. My coffee table has a underneath the table top that I keep all of my large books, magazines, and newspapers.
I also recommend getting a file cabinet! It doesn't have to be big or pricey - a second hand two-drawer one from a garage sale or online will do. All of my papers I file away and now that I have been using it for awhile I don't know what I would have done with all of these papers without it. Since you have lots of closet space you could keep it away in the closet as well. If you don't need both drawers, the second drawer makes great storage space for hobby supplies, electronics/chords, etc.

Dining-
Something I've learned to live without, living in small apartments, is a dining table. I know you already have one, but if you find you can't fit it right, don't be afraid to let it go. Hold on to the chairs - you never know when you need extra seating for guests around the television, or just something to stand on, but consider instead of a dining table eating your meals at your kitchen bar counter, coffee table, desk, or even an outdoor patio table. In the meantime, you can use those extra chairs in places like the bedroom and bathroom as a place to drape a sweater or a towel, or near the front entrance in case you need to set your keys down for a second or need to tie your shoe.
If you'd prefer to keep with the dining table, I'd recommend swapping your circle table for a square or small rectangle shape. It will be much more modular within a small area and fit up against a wall better, taking up much less space.