Relocate your heater/ac controls to the top (which I am guessing is where the cup holder is now) and have two storage cubbies in the lower console.
This imho will get rid of the totally useless cd storage unit and the next to useless cup-holder and give you a little extra actual useful storage area
03-04 have an entirely different cupholders design but still pain in the butt if you want it to hold coffee unless you bring in tsunami / spill-proof cup.