I'd say, stick with the D3000 -- the less expensive camera -- until you have a better idea of what you want to do with photography, and what equipment you want to own to do it.
The D3000 will take great photos, and if you are really getting into photography, you will never want to use the scene modes. Nikon's higher-end cameras (D300s, D3) don't even have scene modes.
The 18-55 is a good lens, and a versatile one. Of coure, the 18-105 is more versatile, but if you're really getting into photography you might prefer the highly-regarded 16-85, or the 17-55 f2.8.
I'd wait to buy a better camera and lenses until you have a better idea of what the camera and lenses you have won't do that you'd like to be able to do.
One last thought on upgrading the camera: If someone told me they really wanted to get into photography seriously as a hobby, I'd recommend the D90 over either the D3000 or the D5000, because it has a built-in focusing motor that both these cameras lack, so you would have a wider choice of lenses down the road.
If you asked whether you should get a D90 over a D3000 for someone who is looking at this as a serious hobby, that would be a harder question. But I think you'd do just as well starting with the D3000 as the D5000.