I would chose the Specialized in this case. There's not enough difference between the components to really worry about it, even if the 2300 is only 8sp. What I prefer about the Specialized is the frame. I currently ride an '06 Allez with the A1 aluminum frame. I work for a Fuji dealer and have had first hand experience with the Newest line, and FWIW I own a Fuji MTB with the same Altair 2 aluminum used the Newest frames. The Fuji frames are soft, I've faced the head tubes and bottom brackets on both bikes, and the Fuji was WAY softer than the Specialized. My other complaint about the Fuji is the down tube. I don't like how it ties into the BB shell. The Newest's I've played with at the shop are quite a bit more flexible than my Specialized. Granted, mine is an older design so I don't know how it stacks up to the '10 model, but the few '10 Allezs that I've seen in person, the design 'looks' better for stiffness, possibly at a weight penalty though.
You already felt the difference in the geometry, the Allez has a steeper head tube angle making the steering twitchy'er,, I like that, some don't. Don't worry about actual weight, there's plenty to upgrade on both to make them lighter, in this price range weight shouldn't be a concern.
One thing to seriously consider though is that the Fuji comes with a compact double, the Allez your looking at is either triple or standard double. So keep your terrain and riding intentions in mind because a crank swap can get pricey fast. --Ryan