When should you upgrade your DSLR?

I have the Nikon D3000, and I'm starting to see some limitations with it. But I'm not entirely sure this is the cameras fault. For example, I take a lot of pictures outside at night, or indoors low light. In both of these cases, the picture comes out dark or grainy, and I have to edit it with a program. The camera can be very slow at taking pictures and focusing in the dark. But I'm still also using just the stock lens. I'm thinking I can get some better pictures if I use a 50mm prime lens (for both low-light and portrait), and get a better flash (like the SB-400).

Also, I almost exclusively use the camera in auto mode, and sometimes I use one of the other configured modes (like portrait, landscape, etc… ), and not any of the priority modes.

Would an upgrade be recommended, or would it be better to try out different lenses and flashes, and learn more about the priority modes first? I think my pictures come out in great quality, but I've seen pictures that looked much nicer (from much nicer cameras, like the D7000).

There are a few considerations.

1) are you at the point where your composition and exposures are intuitive?
2) are you aware that for decades, photographers did NOT feel limited by 35 mm cameras where the only options were to either change lenses or the type film they used?
3) better pictures are not the result of buying different lenses or an external flash. They are the result of the camera user, learning how to use what they have.
4) dark (underexposure) shows you are not using your light meter correctly
5) "grainy" which is actually an attribute of film is caused by shooting at high ISO's. If you are trading possible blur for noise, that is a good thing. Noise can be corrected up to a point in post. Blur can't
6) using a camera in the "auto" mode shows that you still have a lot to learn before spending any money on a new camera (although the D7000 is an amazing one). Look to #1. When you can do that in the manual mode, on demand and shoot with a great to okay image ratio of 4:1, you may be ready to graduate to a better camera
7) if you truly want to shoot landscapes, you need to spend your money on a wide angle zoom like the 10-24 mm before buying a new camera
8) if you are planning on shooting a lot of portraits, the lens you have placed at 55 mm is just fine until you master the camera and lens you have now.
9) priority modes are still a form of "auto". You need to get away from the P&S mode of shooting with a fully adjustable camera.
10) "much nicer pictures" have nothing much to do with the camera, but the camera operator.

This was shot using a 6 mp Nikon D100, generations older than you current D3000.

It was shot in aperture priority mode, while under sail during hurricane season on the way from St. Martin to Tortuga. I had only a few seconds to compose and shoot this one shot.

As you can see, it is slightly overexposed. If I had, had time, I would have used that shot to make a correction and shoot about 2/3rds down in manual, but sailing with only two crew, made that option not practical