My friend, a VFX engineer, shares this frustration with the IMAX version of Star Trek (which she otherwise dug):
Just for future reference, ST was not shot in IMAX, and therefore is not a true imax film. imax is 65mm, 15-perf film, with an aspect ratio of 1:1.37 and a MASSIVE amount of image area, approximately 4x the size of VistaVision (VV is also the same format 35mm still cameras shoot, imagine a negative almost four times the surface area of one that was shot in your still camera.)
Star Trek was shot in cinemascope, an anamorphic format that squeezes the image on the film, but projects it through lenses that stretch it back out horizontally to its 1:2.35 aspect ratio. C-scope is run through a normal movie camera vertically, (90 degrees to a still camera) and exposes a frame taking up four perfs of film - about half the film area of a 35mm still camera.
What Star Trek has done for their imax projection is just stretch their anamorphic cinemascope (1828x1556) image to 3656x1556 and then blow it up by 12% to 4096x1746 where it only takes up 60% of the height of the half-resolution imax - 4096x2988.
(that is, unless they have cropped in at the sides to literally do a pan&scan on the 1:2.35 cinemascope image, ugh!)
The end result of all this unsqueezing and blowing up is that at the very best, you will get an image that has 1/8th the information of a standard imax image. What you see will be much softer, although it may not be noticed by the general public unless they see a side-by-side comparison with a true imax print. Full-resolution imax is 10240x7470 (10k by 8k), btw, but it isn't often used in visual effects because of the sheer amount of data required for each frame.
Other films will be shot in imax and c-scope, with some sequences being full imax, so in the theater the screen will jump to a taller picture for some sequences. I think Batman did it last summer. Normal theaters will only see a c-scope extraction (trimming top and bottom) during the imax sequences.