That's exactly what they're doing. There was a recent article (sorry, no citation) where supposedly the TSA agents said that the more complete pat down is designed to encourage people to stick to the scanners. Lesser of two evils, at it were.
At least there's a choice, of sorts. Hands-off scanner or hands-on pat down. It'd be crazy if the pat down wasn't able to reveal the same items the scanner can, so it makes sense to me, and I'd definitely choose the scanner (I went through one of the trial ones in 2009 and it was quite interesting, though I had no idea what it was at the time).