The Vengeance in this scene is noticable smaller than the one in Locutus' map and the shuttle is right in the mouth of the shuttlebay opening within feet of colliding with the structure so it's definitely not closer to the camera.
I don't see any shadow, but the shuttle/bay size ratio in the second shot (where it's turning to the bay and getting closer) actually does look to me to be almost the same as this:
The enormous shuttlebay is because they like to wing it when it comes to portraying the ship's size, it goes from small to big to small over and over again.
The idea of the shuttlebay changing size comes from Ex Astris Scientia, and was disproven earlier in the thread:
It's all big, all the time. And if it's big, surely the ship must be big to fit it, right?
The circular shaft thing is unknown,
Dome at the top, dome at the bottom. 16+ decks with a wider deck spacing than any prior Enterprise. There is nowhere else it could possibly go, and as you'll see here, they fit perfectly into a 725m Enterprise.
The only way the ship would be smaller than 725m would be if you completely ignore it. Why the need to do so?
Earlier you mentioned the airlocks, here is a comparison of the airlocks on the classic movie Enterprise (and that's a shot of the filming model, btw) and the new one:
when Kirk and Scotty are running toward engineering they appear to run toward the starboard side of the ship veering around a corner then entering the shaft area.
They're leaving the brig, somewhere in the saucer, and are heading to Engineering below.
I was looking at old posts on this thread and that scene directly conflicts with the set floorplan you posted a few pages back. Sickbay is somewhere in the saucer on the backside near the neck's connecting point and the transporter room is probably on the opposite side.
As I told a previous poster, that was the real-world set, not how the Enterprise is supposed to be arranged in-universe. Every single Star Trek series and movie has arranged their sets similarly - for The Motion Picture, the engine room set was just around the corner from sickbay, which is obviously not where they're meant to be on the "real" ship in-universe.
We can't take this ship literally because there are huge scene holes that make it impossible to know which deck they are on.
You can instantly tell which deck the crew are on in every other Trek?
Like in the ship falling scene, after Kirk and Scotty leave the shaft they enter another curved corrider with a turbolift door behind them.
You are aware that the same stretches of corridors represent the entire ship in EVERY Star Trek show ever made? The same corridors will be on deck 5 in one episode, and deck 36 in another.
The movie comic book in 2009 showed Kirk in the lounge on the back of the bridge module, with the huge slotted windows.
The comics also had frequently used the movie Enterprise and one time even the Enterprise-D in place of the correct one. They previously released a TOS comic in which the old Enterprise bridge was covered in 24th century LCARS graphics. They certainly can't be used a reliable resource.
This ship has no consistency what so ever in my opinion, the saucer's center is supposed to have a computer core and this ship doesn't.
Some Trek ships in some of the other series' and movies have had computer cores in the centre of the saucer. Not all, and clearly not this alternate reality Enterprise.
The shuttlebay is also shorter than it was in 2009, it now has the platform shown in ID where they were looking at the advanced torpedoes.
It seemed the same massive size to me, but I'll have to wait for the DVD to be sure. In any case and even if the bay were refitted between movies, two levels of 40ft shuttles line the bay as they did in STXI.
I think what you're calling inconsistancies are just clashes with your preconcieved notion of how the Enterprise "should" be, based on what you've seen in previous Star Treks. As the advertising campaign for STXI said, "Forget everything you know" - Vulcan is gone, James Kirk never knew his father, Uhura and Spock are lovers and Starfleet builds a lot bigger than they did in the Prime universe.