I've been doing the exact same research for my new TJ and keep coming back to the Alpines. I've spent quite a bit of time playing with a friend of mine's 9885 and I can say that the Alpine 988x series of stereos has what I feel to be the best duplication of the iPod controls.
That being said, a few cautions... Most, if not all, of the iPod controlling stereos that connect via USB play the files on the iPod via direct file access, not by streaming the audio in some way. Why is this important? Well, if you've got an iPod Touch or iPhone and have an app that produces sound/music (like Pandora or Last.fm, which many people say will kill satellite radio now), these units will not stream that audio. So you may need to look into a unit that just makes use of a 3.5mm stereo aux-input rather than a USB connection. You lose the ability to remotely control the iPod and keep it locked away, but if playing more than just MP3's is important to you (as I imagine it would be to most iPhone or iPod Touch owners) then it's something to consider.
Lastly, the stereos aren't always up to date on technology if they've been out for a year or two, so many don't work with the newer Nanos, iPod Touch, and iPhones. They may play the music and control it, but not charge, or some combination thereof.
I would strongly urge you to take whatever iPod you have with you to a store like Best Buy (or even better, a local car stereo store where people actually know what they're doing) and ensure that everything works before you pull the trigger.
If you've got one of the older iPods ('Classic', 4G, 3G, Photo, Video, etc) then I strongly stick by my recomendation for the 988x alpines. Check eBay for them - good deals to be had.
-Erik