vaderios said:

Well isnt the second pylon turboil(?) missing from the second shot?

Its a turbolift (elevator). You can't see it as the camera is right next to the one on the right and blocking the view of it. (I've marked the location in Shot 1 where the camera is in Shot 2)

ITs awesome how the lightning and shadows are changing in these 2 images..

How exactly is an animated turboil?

It glows bright blue, but in the movie you can see a shadow that is the elevator car coming to pick up Kirk. However, I think this looks too similar to the engines, so they can be changed to non-lighted tubes if you wanted.

Nothing makes sense from architecture pov :P I guess they looked cool back then :D

I guess so. Its supposed to be a cargo area behind the shuttle bay (which is where the model is coming from). Kirk looks down on it on his way to the turbolift/elevator.

I wish I could explain it better...