We've developed a small embedded device that currently connects over USB to a Symbian phone (S60 framework). Development was... difficult since it was hard to find information on what we needed. Specifically, we developed a simple custom protocol on top of the USB layer to exchange arbitrary data.
We're now looking at new mobile frameworks to support. I'm somewhat surprised initially to discover that some frameworks do not provide low-level access to USB. It looks like Symbian, Windows Mobile 6.5 (but not Windows Phone 7) and possibly Blackberry support for this sort of interaction, but I can't find anything for Android. In general, I'm leery about suggesting any of these as possibilities since I've so few examples of this being done.
iPhone information is a little hard to come by but it appears that we could develop custom protocols if we were properly licensed with Apple as part of their MFi program.
Does anyone have any familiarity with embedded device communication over USB with mobile platforms? I'm curious to know what's possible, why certain platforms seem so problematic and hopefully any annecdotes on successul (or failed) projects.