From the demo on the US Honda site, it appears that the new Pilot's audio connectivity is quite a bit more advanced than the Honda (or non-OEM) iPod interfaces.
Other manufacturers are starting to offer USB interfaces as well. I read a recent review on a new BMW and they have at least had the sense to include it as an option on some models, standard on others. It only makes sense IMO -- I don't know many music players that don't have a USB cable after all. As with most other options (such as air bags and ABS initially, and now traction/stability control systems and keyless starting along with many other things) will eventually trickle down the line to other models.
One thing to be wary of is that the features offered by the OEM and non-OEM iPod interfaces are limited by various vehicle electronics (features and capabilities of the head unit, steering wheel controls, etc.). I have an XCarLink iPod interface in my '06 CR-V EX-L (the Canadian model with leather) that works perfectly fine with my steering wheel controls. However, my steering wheel only has "mode" (which does track advance only) and "volume up/down" (which is obvious). The standard head unit (which has a non-MP3/WMA 6-disc changer and an "AUX" port where the iPod interface connects) allows me to do previous track and track advance with the "+" and "-" buttons. Similar handicaps exist with head unit digital displays that cannot display track/playlist/song duration from the iPod's display (which is the case with mine as well). First generation iPod interfaces merely treated iPods like external disc changers, and simply cannot handle things like playlists, songs by artist, etc. that most of us use everyday with our iPods. It is only recently that the automakers have realized that buyers demand these types of features in our OEM audio systems.... thankfully, their engineers are thinking and marketing weenies are listening when conducting customer focus groups.
All of the iPod interfaces I have seen, used or read about charge the iPod whenever it is connected and pause the iPod once the battery charges. Mine (for example) has a 1/8" microphone jack as well for connecting other audio devices or PDAs.
freddy