I looked at the Trek 1000 and Pilot 1.0 when I was looking to buy a road bike back in May. From what I recall, they are spec'd nearly identically, the only difference being the geometry of the 2 framesets. I chose the 1000 over the Pilot 1.0, as I was interested in getting the bike with the most aggressive geometry.
You are looking, however, at the Pilot 1.2 which offers upgrades over the 1.0 in the way of wheels, shifters and derailleurs. The 1000 and 1.0 have Alex rims and a Sora/Tiagra 8 speed drivetrain, whereas the Pilot 1.2 has upgraded Bontrager wheels and a 9 speed Tiagra/105 drivetrain. Others have complained about the base Alex rims (I have had no issues and have logged over 1000 miles this summer) and the 9 speed Tiagra/105 drivetrain might offer you more possibilities in the way of upgrading components in the future.
Beyond the specs - I would recommend riding each one. The 1000 is going to have more of a 'racing bike' feel while the Pilot series is designed to have a bit more of an upright riding position.