I'd be pretty nervous doing that myself, just don't like the thought of my machine control system halting while the machine is operating due to task switching / battery / etc.
Right now USB is only generally available via the Camera adapter (and it's kinda limited to a few HID types) w/o jailbreaking or specially designed hardware under Apple's mfi program. Hoping that opens up with future revs of iPad, but not betting on it.
Front end sounds more doable, esp. over wifi... Do you really want to replace your machine with the iPad, or would it just be nice to use the iPad to control it?