The Titans keep trying to jack Divine Crusader hardware as a means of keeping it and the SDF-1 as a whole, so as to prevent themselves from being screwed over later. This backfires horribly because the heroes keep beating them up, and the Zentradi, Angels, and Aerogaters showing up really doesn't help their cause. But really, it's because Trieze Khusrenada doesn't like Jamitov Hymen; he even runs interference for the SDF-1 at one point.
Jamitov and Gihren Zabi are secretly using each other to springboard their own plans for space/global domination, while overtly opposing each other with paper resistance.
The AEUG/Karaba become a legitimately recognized military unit under the 13th Autonomous Corps Londo Bell designation, and are more or less given immunity from harassment by being made part of the SDF-1 forces (or such is the idea), and Generals Oka and Igor are their allies in the Earth Federation, obstructing the Titans from screwing them over.
At one point, the Third Angel is making short work of Neo-Tokyo 3 when a man in a snappy suit and a cigar steps out, and manages to fight the Godzilla-sized monster to a standstill with his bare hands. That man is Alberto the Shockwave. He also does this to a Jegan piloted by a Federation mook and destoys it.
The Titans survive past the death of Paptimus Scirocco; in fact, Scirocco never takes over the Titans. Being a plant for the Jupiter Empire, he takes his followers from within the Titans (Sarah Zabirov and Yazan Gable among them) and defects back to the Jupiter/Balmar alliance late in the game.
The Machine Cells are the Earth-based version of the Aerogater's Zyflud crystals.
The post-Black History earth has very low prana, stunting the effectiveness of the Masou Kishin mechs.
Speculation: though the Aura Battlers aren't in Alpha Gaiden, since Byston Well tech runs on a similar premise, it can be safely assumed they would fare poorly as well.
The Earth Cradle was a halfway finished backup plan of Bian Zoldark's that was scrapped, and later continued by the Nubia Connection for its leader, Khamen Khamen. Khamen uses it in case his operation to blow up Jupiter gets royally screwed. The Ancestors are born as a result of the security system of the Earth Cradle going haywire, screwing Khamen over by default.
Khamen is on speaking terms with the Moonrace leader Agrippa Maintainer and Dekim Barton, until he kills both of them when he no longer needs their help.
The Mariemeia Army is a remnant of theOrganization of Zodiac collaborating with the Titans obstensibily to get the remnants of the Romafeller Foundation back into power. In reality, they're lying through their teeth and planning to use Operation Meteor to blackmail the Titans and Preventers into submission, and want to subvert Operation Aegis to save themselves and their supporters. The Titans are pretty much doing the same thing.
Midgard attempts to hijack the GP-02 Physalis for use as a trump card for the Ghingham Army, but is stopped by the Preventers.
The Innocent and Moonrace are bitter enemies, despite both having fled to space after the Dinosaur Empire ravages the planet.
General Bat somehow can pilot the Shin Getter Robo. The Alpha Numbers get it back with the help of the ∀ Gundam.
This may be a possible Shout Out to the Getter Robo manga, where three Dinosaur Empire soldiers stole the Getter Robo G and were able to pilot it without any real problems.
Char's reason for colony droppingAxis in Alpha 2 is more or less born out of seeing the records of the Black History. He repeatedly lampshades through the rest of Alpha Gaiden that he's seriously wondering if humanity really is doomed to eternally screw themselves over and over again, which provides the convenient bridge to his Face Heel Turn in Alpha 2.
The Frost Brothers are pulling off the same scheme on the Moonrace and the Innocents as they did in After War Gundam X, which is essentially get both sides to kill each other as payback for them not being picked as anything other than Category-F Newtypes.
Egret Fehu seems to know that if the shockwave successfully devastated Earth, the Mycene Empire, Dinosaur Empire and their army of mechabeasts will attack. As a countermeasure, he baited the Mycene Empire into attacking South Atalia, knowing that Tetsuya Tsurugi, the person with the most experience in fighting the Mycene Empire and the best pilot alive, is the only person left on Earth amongst the Alpha Numbers, who will defend the place. As a result, he used his battle data as a reference for his project that results in the creation of the Machinery Children.
Super Robot Wars Alpha 2
The Zonder forces try to go after Orphan, who are deathly afraid of the Zonder.
They also try to go after Photon Power Labs. They avoid the Getter Rays because it causes living beings to evolve, something the Zonders consider an abomination.
Koros and the Meganoids want Beamlar to help Don Zauser's plans.
For some reason, Heero Yuy appears to have the most number of non-generic battle quotes: this includes at least two against Londo Bell members (at the first two stages of Arad Balanga's route), several against Zechs, the Titans, Zeon and Neo Zeon soldiers, Mechasauruses and Battle Beasts, battleships, Haniwas, against Newtypes, Haman, Char, Yazan and at least two against Irui Gan Eden. This is due to Heero's voice actor Hikaru Midorikawa being a big SRW fan and occasionally does voicework for the games for free at times.
Early in Super Robot Wars Alpha 2, the scientists from throughout the Federation are meeting for the first time since the Balmar War, joined by Relena. They've all been sent with the Taikuu Maryuu as representatives of the Earth in meeting with the new aliens, which call themselves the Balmians, on Mars. The meeting ends in failure, with Richter thinking that the Earthlings poisoned the drinks that killed his father. Richter killed Isamu Ryuuzaki in response.
The One-Year War, the Balmar War, and the shockwave from the ultragravitational collapse caused Beamlar to awaken.
Shinji decides to reject his father's ambitions and declares to the world that he is his own person. What follows is Shinji piloting his Eva to fight Gendo who is...also piloting Eva-01. It's not particularly clear if this is all in Shinji's head or simply Instrumentality messing with physics.
When Noriko and Kazumi are going to explain the spec of the Eltrium, Ryusei mistakenly recall it as Nani? Naze? Top!. Raideese correct him that it's Science Corner and turn out that Rai has watch lot of mecha anime recently, in hope to understand Ryusei better.