Am I the only one here who thinks there's a logical explanation for every deviation from the mainstream universe, because some days it awfully feels like it. While I realize 343 had to take some artistic liberties when they were designing Halo 4, I personally believe there is a logical explanation for everything they did... well, mostly everything.
My own headcanon suggests that the Jackals in Halo 4 belong to a subspecies of Jackal I would call [b]Monitors[/b], who were simply Jackals who went down a different evolutionary path than the common Jackal (the subspecies I dub the [b]Vulture[/b]). Monitor Sniper helmets are different because Monitors don't have the elongated snout of the Vultures.
Stuff like that. So, do you think there's an explanation for everything?
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Obligatory lolHalocanon. The thing with Chief's armor was an issue back in 3 also, as his gloves magically transformed aboard the Keyship (though I wouldn't know if this was explained in the comic). Cortana retrofitting everything on the ship wouldn't make sense either, as it would be miraculous if everything she did turned out to be the exact same path the UNSC took. That could have been a cool plot point though; it would have been similar to what Durandal did with Boomer. I did notice that they were thoughtful enough to not put any weapons on FUD or its wreckage that weren't in Halo 3 (No DMR). For that reason, I think we're supposed to take things as an artistic upgrade, but no real difference to the characters. This has happened through all the games of course, for instance the Halo 3 battle rifle has a longer barrel and is overall a larger weapon than the Halo 2 BR, yet the Halo 2 BR is more accurate (and the flood in High charity carry the "new" model).