Well I happen to own a Nikon D3000, and yes it does underwhelm only do to the fact that I thought it would be more powerful than the D40X/D60 I once owned. But I can get the same look from all the cameras, and the images are good. Plus for low light photo the D3000 lags a bit behind when it comes to noise.
The D3000 isn't much of an upgrade from the D40X/D60 and you are well suited to get the more visually and technically advanced Nikon D5000. But in my true opinion once the techniques of photography are learned you can get good images from any camera. Yes the GUIDE MODE is too basic (School stuff already learned), and instead they should have (If possible) an in camera Users Guide instead of the CD Manual.
Plus with the D5000 you get more flexalbe software, especially if you want to upload a customcurve to the camera, or use custom settings in the camera. The D3000s software capabilities are slight, and there are no real customizable controls or software, save just uploaing your pictures to ViweNX or Nikon Capture for RAW.