I've tried a number of hex-editing tweaks to the mission files and so far none of them have worked.
I tried replacing the AATs on Rhen Var and Naboo with MTTs (editing both missions.lvl and the actual
map .lvl files) and in most cases it simply crashed the game. The best result I got was with the Naboo
map where I could get the game to load, and the MTT actually showed up on the CIS spawn point vehicle list -
however, the vehicle did not actually appear in-game.
I've given up for the time being, hopefully Pandemic will release some official tools in the future (the indications
are that they will, though -when- is another question), and the game still has plenty of replayability even without
the missing vehicles.
Going by some of the filenames, the "Imperial Transport" seems to be the Shuttle (3-winged design) rather than the actual Transport (a larger, more boxy-looking ship).
I've no idea what the Rebel "Hovernaut" is, but in the maps it is the Rebel equivalent of the AT-AT/AT-TE/MTT, so presumably it is big, heavily-armed and acts as a mobile spawn point.
I do think that the vehicle lists for some of the maps could do with tweaking - apart from the 3 unused vehicles, it's a shame that a number of vehicles only appear in one map, the hailfire droid and skiff for example. I agree that the battles which are based on events on the film (e.g Endor, Geonosis, Hoth) should only have the vehicles which were actually there, but the "non-film" battles (e.g Rhen Var, Clone Wars on Tatooine) could definitely do with a greater variety of vehicle types.
By the way, I am not really what you would call a "Star Wars fan" though I do like the "style" of the SW universe. I have seen some of the films, but most of my knowledge is based on playing other SW games such as the X-Wing series, so I apologise if I'm not too knowledgable on some subjects