Edit. and henke37 said most of what I would, oh well I will leave it up.
The GBA has no 3d hardware (or software abstraction/standard) to try to match up against/watch like you would on most 3d capable systems. Most of what you see will be pure software (The game Payback is a good example I believe and https://www.youtube.com/watch?v=LfYZ08L4qY4
is also one of my favourites), isometric/2d trickery/prerendered or the GBA's kind of like SNES mode7 like effect aka affine transformation ( http://www.coranac.com/tonc/text/affine.htm
), the last two being the more popular by far as software 3d on a system like the GBA is the stuff of programmer nightmares. I am not sure what this would be and a quick look at a gameplay video does not have anything quite jump out at me (the changing colours are easy enough to do in palette animations), though the aliasing and pop in could mean things, the camera is not quite fixed, most structures appear to be simple polygons (suggesting a fairly low limit) and those pinball style bouncers warrant some attention as well. I am prepared to see that be an actual software 3d engine though.
Are you familiar with general 3d imagery and/or the computer hardware that runs 3d? It sounds like you know the higher level stuff but might be hazy on the lower level stuff (and for the most part the lower level stuff is a bit like learning assembly to be a general programmer today).
Equally I should note that levels and models are not always one so you might have to decode a level format, or a level format composed of blocks, and a layout file, doubly so as the layout will have to account for different types of terrain/moving obstacles.
Even if the GBA did have 3d hardware then I would probably still make a basic level select cheat (well infinite time first so you have some room to breathe/test) and then debug that. This is not likely to be an easy hack.