I thought they would maybe keep the elite here just to keep a bike close to, but not over the $1000 mark.

Too bad nobody has answered your original question; why is the '06 so much cheaper than the '05 as they spec out the same parts?

Another question for you:

Did you take a close look at the brakes and brake levers? The specs for all models call for alloy brakes and levers, but the Comp and Elite I saw in the store both had alloy brakes (Tektro of some modes), but plastic brake levers.