Can't say I saw any size discrepancies this time. Alcatraz is practically microscopic under the hull (didn't bother spoiler tagging that as it's in every single trailer)
Seeing the Vengeance slicing through the city really cements the colossal size of the thing.
As for the Enterprise, shots of the ship next to shuttles again (which are bigger themselves remember) and even tiny swimming people clearly backs up the 725.35m aswell.I don't want to open up a can of worms in Baz's thread (again), but as a small insight into VFX production (a field I've recently entered and have a lot of friends in ;))...
Nowadays for film and even TV, finalized 3D models are built accurately to 1:1 scale in the 3D environments (I feel sorry for whoever had to handle the Narada!). So if that's how big they say the ship is (eg the Enterprise is stated to be 2379.75 feet/ 725.35m in the bluray features at least twice [Screenshot for anyone without a bluray player:
http://2.bp.blogspot.com/-YENremF4m0M/URATyW1Z1vI/AAAAAAAAMmE/LPPoT0K9r2w/s1600/Star+Trek+Consititution+class+comparison.jpg] and in the Art of the Film book), that's how big it really is.
Again, the only clear discrepancy to the large scale I've seen in either film is the shot of the shuttle taking off while the Ent is being built. This was likely to allow for the tight camera movement swinging up to reveal the reg number on the nacelle. We often have to bend the rules a bit based on what the director wants a shot to do. It's his film after all.
Every other shot we can judge from consistently show it to be the larger given size. Even the very first teaser trailer shows the workmen welding it to be tiny on it's hull. Plus, the Enterprise isn't a Tardis, those large cavernous interiors have to fit somewhere.
As for the phasers/disruptors/nasty beams of doom from the Vengeance. I don't think length matters that much. Remember TNG phasers were usually a looooong continuous beam.
