Hi Ryan,
Here are a couple suggestions for taking better bonsai photos
1) Background
Photograph your tree with a plain background, as uncluttered as possible. For medium or small size bonsai, one of the folding cardboard portfolios that you can find at an office supply for about $5 would be great. They come in black and white and measure about 3x4 feet when opened. They are designed for science fair type projects and made of corrugated cardboard. The one here is called a
Project Display Board by Hunt. They make a higher quality one that has foamcore, but it doesn't really matter.
With the distracting window and shadows, it's' a little hard to tell what is tree and what is not.
Add light:
The single camera mounted flash is has a nasty habit of projecting shadows on your backdrop. You can decrease the intensity of the shadow by photographing outdoors in indirect sunlight or shade, and using the flash to provide just a little fill. You can also move the backdrop farther away from the tree. Any shadow will grow in size, but it will also become more diffuse.
Another possibility is to use a pair of utility lights with 12" aluminum reflectors that you can find at any hardware store. Position one on either side of the tree and the shadow behind it will be significantly reduced. If you have the opportunity, use three lights and direct one right at the backdrop from above or below.
If you are planning to post the tree on a webpage, a camera with a lot of resolution isn't critical, but you want it to be sharp and in focus. Step back away from your subject and zoom in if the camera has a zoom lens. If not, you can crop your subject after shooting and still have an acceptable image for a web page. If you get too close to your bonsai subject it can become distorted and unappealing.
Best regards,
Matt