I recently had an App rejected too under 10.6 because they said it needed to use more of iOS' features.

I replied back letting them know, that the App was greatly enhanced by the multitouch interface, and asked if they had any suggestions. The App Store reviewer was actually very nice (almost excited that I wrote back?) and reasonable. Their biggest concern was actually relating to lack of iPad specific features/views on the iPad version. It seems Universal apps are reviewed a little more harshly.

I think they have a lot of rules, and sometimes it's hard to keep up the manual review process when they don't see the immediate value of the app. In general, they are quite nice however and will let you know what they are thinking.

For what it's worth I opened sourced the rejected app anyway https://github.com/dmitric/tap-pad-ios