Hi Mark,
>> However I would still like to use the existing templates settings for Mobile vs Desktop to have different settings for hiding things, etc. etc
The IsMobile() method extends a long way beyond just themes and include/exclude options. The Mobile framework is build on Jquery Mobuile, and the Desktop on Jquery UI, so the underlying code is quite different as well. So your idea is good, but supporting it would be very non trivial at this point.
Cheers
Bruce