The thing that has always bugged me about the whole Clone armor thing in the prequels as opposed to the OT armor is not so much the camo or the different "battle gear" (such as the ARCs or the jet packs), but more the sudden appearance of rank delineation with the color stripes and whatnot.
In the OT, we had Stormtroopers. As Randal Graves once said, "Killing in white uniforms" and they knew nothing about installing toilet mains. There were different subsets of soldiers for special weather conditions (Sandtroopers, TIE Pilots, AT-AT Drivers, Snowtroopers, and Biker Scouts), but all of their armor was identical (well, the Sandies' pauldrons were ranked, so there's strike one on my theory). My point is, that within the normal ST ranks, there was no delineation of rank shown by their uniforms. It was all generic and the whole "faceless" nature of the Imperial infantry was much more pronounced.
Now, the prequels roll around (or we find out the ST origins; however you like to put it) and we've got Yellow, Red, Green, and Blue stripes to delineate rank in AOTC, then we've got full blown color schemes (those blue guys that are following Anakin in the trailer) and again, multiple rank designations. It just doesn't make a whole lot of sense to me; even if you're a mindless automaton, doesn't the chain of command theory still hold true? I envision these grand Stormtrooper arguments aboard a Star Destroyer like the ant farm on the "Deep Space Homer" episode of "The Simpsons:"
"PROTECT THE COMMANDER!"
"Which one's the commander?"
"I'M THE COMMANDER!"
"No you're not!"
"Yes, I am!"
Of course, my own personal theory is that in addition to this posthypnotic thingy that Palpatine pulls on the Clones to have them turn eeeeeevil, it also somehow eradicates any individuality they may have developed during the Clone Wars, and a rather unfortunate side effect is that they are now all completely cross-eyed and cannot shoot straight. Kind of like a giant "DURRRRRR!" button that Palpatine can push or something and keep them in line.