Cubase 6 is actually more customisable than previous versions of the program.
Firstly you can design your own palette of colours by clicking on the Select Colors icon on the toolbar and selecting ‘Select Colors’ at the bottom of the list. This gives you a standard palette selection interface. Once you have set up the colours you need you can save the current set as the program defaults, if you wish. Contrary to what JM mentions above, I don’t think the colours are overly difficult to set up. You might have to spend a bit of time on it but then if we all want something different with colour then it has got to be open-ended. One of the eternal dilemnas of software design - how to keep the thing simulataneously flexible, customisable and easy to use.
Next you can manipulate the look of the colours and waveforms in the event display using Preferences / Event Display / Audio. For example setting the waveform brightness slider to minimum gives you a black waveform or setting it to max gives you a white waveform. Setting this slider to around 33% combined with the waveform outline intensity slider set to around 75% gives you a two-tone waveform / backgound colour mix and suits many different colour schemes. You can do similar things with the display of MIDI events.
Preferences also gives you the option to customise the general colour scheme of Cubase and the intensity of various elements of the work area.
So, in my opinion, colour management in Cubase 6 is far more flexible than it used to be. You just have to know how to do it and spend some time setting it up to your own preferences. I think the essential ingredient is the palette of colours you choose in the first place. This can radically alter the look of the events in the display. Admittedly not everyone likes the graduated colour background of the events.