One thing, do you want to be able to control you ipod, or just get the sound off of it. I own a small mp3 player (non ipod) and just use an adapter for my alpine HU. Works fine. But some people want to be able to control it off the deck, or through wheel contols, etc.
If you are set on stock, you can check out Peripheral-http://www.peripheralelectronics.com/sitemap.asp My dad has that installed on his s2000, he loves it. It's a little bit slower than using the ipod manually but it retains all the stockness, all the controlls, and all that. My dad is an "aftermarket hater" and is pretty impressed so that alone tells me it is good.
On the contrary, i've never heard a stock system that impressed me so a good HU could be the foundation for a much better system. You obviously will spend more (or should imo) but then the adapters are only $15 or so. That's the route i would recommend.