It depends on what you do in the office and how much you want to spend, but I would: Get rid of the rug entirely and leave the floor au natural, but add a desk chair mat under your chair to protect the floor. Add a few tall shelves or bookcases, depending on what you need them for (files vs equipment vs books) -- Ikea has some nice options that aren't expensive and are easy to assemble. I'd add colour to the window covering (different drape? coloured tie?) and then decide if you want art work/photos and/or a corkboard/white board. If your peripherals (like printers, etc) are small, you may want to consider something like Ikea's Kallax series, because they could fit in some of the boxes, while you use others for books or baskets. I wish I'd thought of that before I got the storage unit I did.

Wow, lots to do. Very exciting. Suggest you break this post up to get more responses.

I’d frame the opening to crest a visual gateway between the areas. My drawing skills aren’t the best (and now I’m proving it), but here’s an inspiration picture along with how it would work in your space. Then I’d hang one (or more) small round mirrors on the right side wall. Round will soften the squares of the doorway and mirrors will bring in some light.

I don't know anything about your job, the tasks you need to perform or your relationship with your boss, but I am going to make my recommendation based on these two comments 1. You recently started this job, would like to paint it a dark color, but my boss thinks it will make the office feel even smaller. 2. Mainly I want it to feel tranquil, welcoming, and helpful for concentration. Do not paint your walls a dark color. Your new boss has given you an opinion. Your not going to make a great impression by doing something they have advised against as one of your first acts. Do not paint your walls gray or black. These are great colors for power negotiations, but not great for concentration or productivity. If you are doing repetitive tasks brighter, more stimulating colors help with accuracy. If you are doing more complex cognitive tasks a softer blue and green both enhance concentration. To make the room feel masculine I would use a mid toned grayish green or a mid toned slightly grayed blue without overdoing the gray or going excessively dark. I would pick the art for over the computer first and then pick a wall color that complements the colors in the art. I would get art that has some richer colors and higher contrast to help balance the calming effects of the wall color. If the art is primarily blues and greens and the wall color is blue or green you will want a couple of items with some orange or yellow to add warmth. Hopefully the art has some warm tones, then you can use something on your desk that has some warmth.