What makes this tiny room look incredibly busy and as if it was all just thrown together without much consideration are the following things: innumerable cords on and around the desk, bookcase overflowing with books (the upper two shelves have caved in), furniture of different materials, random pieces of artwork, stuff just laying on floor. This is what I would do. Make the wall where the desk is the "storage/work" wall. Put the bookshelf against that wall, and then replace the desk. Though I love the desk that you guys have now, the fact that it is transparent means that you can see all the cords. Replace it with lighter wooden desk (like your chair), that comes with storage -- solves some of you document storage needs. Get some simple larger storage pieces of furniture, where you can store your shoes, weights, etc. behind a cloth cover. Use similar cloth cover to cover the books, and hide all that busy-ness. I would also use similar cloth to cover the sides of the sofa/bed, because that dark brown really does not work with lighter wood. Not sure whether you can paint, but if you can I would suggest perhaps light, pastel green, which would work wonderfully with light, transparent window curtains, and light beige cloth covers for storage and sofa sides. Hopefully, this helps.

oh also I would get rid of the artwork (unless you really love it). It dates the room. And add more light to the room.

Your husband can put his clothing and uniform accessories in clear storage boxes that slide underneath the futon. Clear boxes will mean that he can see what is in the boxes and it will protect his stuff from getting dirty.

Cutting down on the clutter would make the room instantly feel more liveable.

To add some cheerfulness, try buying a few colorful throw pillows for the futon and some draperies for the window. You need not take the shutters off -- just hang the curtains so that they fall on either side of the window. Something light-colored and airy, like linen or tussah silk would be beautiful for the drapes. If you get them at a clearance sale they need not be expensive.

Likewise, a nice rug will bring some texture and pattern to the rather depressing floor. (Is that linoleum?) This would also make it look more like a sitting room than a junk room.

Once your husband's clutter is stored away under the futon, get a few (very few!) accessories to put on the top of the two chests of drawers you have. I suggest candlesticks.

Check out Etsy, Society6, or a local flea market for some art that you love. Art really pulls rooms together and makes them feel more comfortable.

As a last piece of advice, consider some kind of cord management system for the desk. The desk itself is lovely, but having cords everywhere makes it look untidy.

The desk is lovely, but it looks out of place in this room. I'd suggest getting a new desk, with file cabinet drawers. Scan as much paper as you can, and two file drawers should hold everything that you need to keep copies of. That would remove one piece of furniture and instantly give the room a little breathing space.

This room seems to have all the "rejects" that won't fit anywhere else. It's difficult to get a clean, uncluttered look when you have a mishmosh of furniture and general "stuff."

One thing to do is get the weights and other gear into some sort of storage--a bin, a basket, even a nice tote bag--those LL Bean canvas totes are good for this sort of thing. Or something that can fit under the futon. Or hang things from the walls--even the backpack would look better if it was on a hook. But the more stuff you can fit in enclosed storage, the better.

Consider moving the bookcase to another room, or buying a second, smaller bookcase and splitting the book collection between two rooms. Then the empty shelves in this bookcase could hold some of the things that are on the floor now.

I think if you re-think the furniture a bit, and limit the number of wood colors as much as possible, get a desk with storage and put as much of the stuff as possible behind doors or in drawers, it will help a lot.

Then pick a color scheme and add a rug and curtains and some matching pillows on the futon. That will make it seem as if you planned the room, instead of just letting it happen.

Thank you everyone for the fabulous suggestions! This room is precisely a mash up of everything that we didn't want to put in the main living area. We are planning to get a new desk with a built in filing system (as mentioned above) and the bookcase is leaving! Although I do love the desk, it is a bit too big for the room, so it may have to be donated. We have since put the weights into a basket, so that looks much better. Thanks again for your suggestions; it was much needed and very helpful!!!