It's a tough call - you'd have to get some actual numbers on trade-in from dealerships to give this any more thought. If you've got the extra money laying around and want the '06 upgrades, ask yourself if $2000 for 9,000 miles is a good deal. I'd say it is considering how bad depreciation is on new cars. But, is it really only going to cost you a couple thousand?
What if you put in the Pioneer Nav headunit w/ ipod connection? (I love that thing) Or not even a nav headunit, just one with an ipod connection? If that would hold you over for a while with your ipod issue, keep the stock radio, then when you find the perfect trade-in deal on an '06, put the stock radio back in and move the new headunit to the '06.
Regardless - the choice is yours to make! Good luck whichever way you go.