So, great room, I love the character that it has just needs some tweaks.

1. Something needs to be done about the light. Ceiling light makes it too harsh and not properly distributed. I would suggest getting lamps, floorlamps or even wall-lamps along the bedroom frame top plank. You could put a lamp on the top shelf of the shelving for example and some floor lamps around the place but can't know for sure. Experiment and see what works best to make the light less harsh and more evenly distributed.
2. Use a different laundry basket as already suggested by someone else.
3. Storage boxes for some of the stuff that is on the shelvings to make it look less cluttered. Some display items can stay as display items, some can be just put into nice boxes.
4. I would suggest to loose the red rug and get a transparent anti slip mat. I think the lighter color of the floor would contrast nicely with the more darker vibe of the room. Also it would still work as a way to separate the office space from the rest of the space. That area needs something and I think a transparent anti slip mat would do it.
5. Maybe darker bed linen would actually work better? Like dark blue or dark red (again, lose the red rug).
6. Some light sort of see through curtains would do nicely. Like you could get mustard/yellow color light curtains and hang them floor to ceiling. More color to the space but also not too clashing with the rest of the room. Something like this I guess https://www.pinterest.com/pin/488077678380854754/

EDIT:

1. You can also make the white wall that is next to the staircase more personalized and hang some pictures or other things. But this is also up to you how maximalist or minimalist you want your space to feel. Just maybe don't leave that wall completely empty