pioneer p6000ub
Just put one in my daughters car, connected to the stock amp and speakers, with a new center channel. The ipod interface is built in--you control from the hed unit via a usb cable, and there's also a secondary mini-stereo plug input.
Check the reviews on Crutchfield, very good. The model was just discontinued, but they're still in stock at Amazon. Don't know about the successor model listed, it's a little more than what I paid for the one I have.
I haven't installed one of these these things in ten years, and I remember looking about 18 mos ago and the ipod interface was usually an addon. The current prices and capabilities are amazing. I may even dig out my old db meter and try equalizing the car.