The integration with iPod is already pretty strong on some head units. Alpine does it the best, which is good because they are the only ones out there making head units worth buying these days anyway. I have an ida-x305 that I had in a Grand Cherokee for a while and now moved to my Miata, and that works extremely well. The system for selecting a song isn't 100% eyes on the road, but it's pretty good requiring only a quick glance to know what you're doing. The wheel they give you works well and has tactile feedback, and you can set up fast scrolling through your library in a couple of ways that work well. You can adapt steering wheel controls pretty easily so previous/next, volume, and (maybe) source is 100% eyes free. They integrate with pandora too if that's your thing.
Alpine has since changed their design a bit, especially the screen, and I am concerned about it. I want to get a new one for the app-based eq and integrated bluetooth, but I'm nervous that it won't be as easy to navigate. My buddy told me it was, so we'll see when I check out his next week.
I also have a top-of-the-line double din Kenwood from a couple years ago. The integration on that is good enough, the main problem is that the head unit is slow and underpowered for the amount of stuff it does. Using the touch screen to scroll music is also just a really crappy setup, especially when things are slow and flaky. Once you find what you want it's fine and the steering wheel controls work with that as well, but its not as good as the Alpine.
I like my wife's BMW for integration a lot as well. The newer iDrive systems are excellent and the wheel they give you to navigate is right at hand and allows you do do things without taking your eyes off the road. The way they navigate an iPod leaves a bit to be desired...if they redid the software a bit they'd have the perfect system.
My FJ will skip/next with a bluetooth connected phone running spotify, which is...ok. It does allright with ipod integration as well...as well as you can do with a small low res screen.
I think what I'm getting at here in the end is: touchscreen bad, physical wheel good.
My main problem right now is that I (finally) re-ripped my entire music collection to flac over the winter and I'm trying to find a portable that will play those and integrate into the car. Been scouring the head-fi forums the last few days...dx90 seems to be the leading contender.
I need to reckeck and see if the kenwood will play flac off a usb drive directly, but that still leaves portable and the miata to come up with a solution for.