I would suggest you to first move your bed to a different wall where you wont have a problem with the window not being in the center but if you don't want to do that then you can go for asymmetrical nightstands, one being slightly bigger than the other. For color add a roman blind (vibrant and colorful fabric) to the window. Or you could also go for a different color for the wall behind your bed.

Accessories to be added:
Some matching throw pillows and bed cover
A plant
Lamps on the nightstands (could be asymmetrical)
A few paintings or framed pictures

To cover the closet door, you could use bamboo blinds or a nice matching curtain properly hung using a curtain rod.

First, since this room is the only space that is all yours in the apartment, you should think about how you want this room to feel? Bright and colorful? Soothing and relaxing? Boho chic? Energizing?

Then think about what you will be doing in this room? Surfing the web? Watching TV? Sleeping? Reading? Entertaining guests? Working out? Getting dressed? You need to identify the uses of the room and make sure that you have the supports in place to do all those activities.

So you might want a dresser, for more storage and to hold a TV on top. Or a bookcase, for books and for storage, in baskets or bins, for other things. Nightstands to hold a clock, phone, lamp, water glass, book. Or you might want a comfy reading chair with a floor lamp and small table for a cup of tea/gin and tonic. Figure out what you need to add to the space.

Then work on colors. If you are keeping the quilts on the bed, I'd use those as a foundation. Change the carpet if you don't like the color. Either go with something neutral or pull a color from the quilt. Add curtains to the window, again pulling a color from the quilt. The closet could get a matching or contrasting curtain, or a bamboo shade.

If you've figured out what style you would like the room to have, then you can work from there on the matching or unique nightstands. Do get some lamps in there for better lighting.

Maybe rig up a cover for the dog's crate, or stash it under a small table. Find a basket for all the toys to keep them corralled.

Take your time and find some artwork that speaks to you and your style for the walls. Once you have things in the room that you have chosen and that you like and that reflect you and your style, I'll bet the baseboards and door will fade into the background and not bother you so much.

I think previous posters have made good suggestions regarding other furniture, accessories, and art you might add.

I suggest hanging curtains to "center" the window, like this:

http://sawdustgirl.com/2012/01/24/how-to-trick-your-eye-into-thinking-that-a-window-is-centered/

Mount the curtain rod almost to the ceiling to make the room seem larger. Then center your bed on the wall to complete the look.

Also, get a tension rod and use a fabric you like as a makeshift closet door.

Another post recommended using fabric or a curtain to cover the closet using a spring loaded curtain rod. It will look great.

There are definitely some great ideas to hide dog crates that look wonderful and are functional for you too! See below:

http://www.designsponge.com/2010/04/before-after-dog-cratedesk-jens-laundry-room.html

http://www.hgtv.com/video/dog-crate-cover-bench-seat-video/index.html

Unless your landlord is paying for the carpet, I'd buy an area rug to hide the majority of it green carpet, and you can bring it to your next place.

For the walls, shop around for a couple nice pieces of artwork, framed posters, photos (but not too many, you don't want to clutter the walls and make the space feel small)

Good luck!