I'd go for the Giant (i'm biased) based on the fact that frame material is superior. When you get the money, you can always spend a little money here and there to upgrade to the components that you want. Keep in mind, that the Giant frame by itself retails for over $1500.
I owned a CAAD5 bike for a week before returning and buying the Giant. I liked the look and the value of the cannondale, but when I was riding it, it was too stiff for my enjoyment. You can swap out saddles or tires, but nothing will make more of a difference for the "feel" of the bike than the frame. Keep in mind that the Cannondale has a very aggressive geometry coupled with a stiff aluminum frame. The Giant TCR also has a relatively aggressive geometry but the carbon helps out a lot with comfort and vibratioin reduction.
Also, you won't feel a huge difference in different components if you're new to road biking. You'll feel the biggest difference with a carbon frame.
I would opt for the 10 speed 105 of the 06' TCR vs the 9 speed 05' though. Sheldon brown says that it is very likely that the 06 105 groupo will outperform higher groups because of newer technology.
Ride both, see how they fit. Don't forget to take it to some uneven pavement... that's where the carbon will stand out.