The exactly three things not totally stock on my '04 is the cruise control, needed to avoid speeding tickets on trips, the custom clamp on front license plate bracket I built, I couldn't bring myself to drill the front bumper, and the positive battery cable connector, I made a $3 fix as opposed to paying $100 deductible for a new $400 battery cable.
I have driven my car over 48,000 miles since new and it is still under warranty.