The fact Jigoku-hen reveals the events of Mobile Suit Gundam: Char's Counterattack is underway means Char Aznable has gone against his previously established word of ensuring the Black History will not happen on his watch. Players had already declared him a Hypocrite and a liar, except if they recall the events of Char's Counterattack, that's exactly what Char is (he lies about not Colony Dropping any more asteroids after The Federation hands him Axis, but he does it, regardless).
Though it likely deals with the memory muckery that has affectd all of ZEUTH and ZEXIS seen in the game.
As it turns out, Char really DID keep his word in the end, and he was using NeoZeon for his own goals of helping the heroes.
Wayne's willing to attack female pilots just as equally as male ones BECAUSE he's a Feminist and he sees it as treating them as equal.
Australis's theme is a somber remix of Gaiou's theme because they're both Dimensional Generals.
During a scenario, Basara senses something weird about Kaworu and asks who he is. He replies that he's a messenger, sent to this world by the descendants of -the people of the ancient wandering white and black moons. Kaworu wants to hear Basara's song because Basara is the one "he" has been waiting for. The world Kaworu was once in died and was through the song of a mechanical god reborn as a promised land wished for by those who lived in that world, but that promised land too was unable to escape from the cycle of death and rebirth determined by "him", and this world they're in right now is what was born after the last one died. Basically, everyone in the Super Robot Wars MX world is now dead.
The Mayan prophecy's mentioned throughout Jigoku-hen. Blood of Beasts (Team D), Fellowship of Water (Aquarion), Destination of the Wind (Simon), Civilization of Fire(Newtypes) and the Brilliance of the Sun (Tetsujin-28). However, there's no Moon age despite there's so many Moon themed mech around (Zambot 3, Turn A Gundam, Gundam Double X). Also, why isn't Daitarn 3 the Brilliance of the Sun? Banjou Haran even says it as part of his catchphrase.
Z-BLUE, specifically the Celestial Being portion, already had to deal with both Al/Hal and Soma/Marie. Why didn't Celestial Being realize that Ambriel is Suzune's Split Personality?