I would have agreed with that before I owned and rode an '06. The '03 engine is much more thrilling; the '06 is vastly more useful, and the bike is noticeably faster because of it.
BTW, wouldn't a 03 YZ450 motor in a 2007 chassis be the perfect bike? (with an auto-clutch, of course)
Your "butt dyno" is lying to you.