Our bikes also came with Bontrager Race Lites and we got 4 flats in the first three weeks we rode. We replaced the tires with the Michelins and have 2400 miles each on two bikes with only one flat, and that wasn't even discovered until the following morning. The tire is a bit of a rough ride - we have been going 20PSI in the front and 10PSI in the rear under what Michelin recommends to soften the ride.
I've also used the UltraGatorskins with similar results but only went about half the mileage before I sold them (and the bike they were attached to).