Common Knowledge: The infamous "Full Possession Cybuster can access the Akashic Records and erase his enemies from existence!" rumor subsisted for a very long time, started thanks to a mistranslation in the fandom's early days. It finally died when Revelation of Evil God allows use of the Super Mode, and while powerful, the Cybuster is not a Reality Warper.
The Cybuster can access the Akashic Records: it's just not a Reality Warper as rumored.
Foe Yay: Masaki Andoh with Shu Shirakawa; in fact, the feeling is mutual as Shu remembers a lot more things about their feud when he comes Back from the Dead as an amnesiac in Super Robot Wars EX. In particular, he regains some memories simply by looking at the Cybuster in Dark Prison.
That One Boss: The last scenario of Masaki's route in the Second Super Robot Wars Original Generation has the player fight Feilord Grania Bilseia and the Duraxyl. At this point in the game, this boss is more accurate and powerful than previous enemies, has the "Move Twice" pilot skill and the first boss in the game to make use of a MAP Attack when the player has very little in the way of credits to upgrade allied units with, upon getting hit. A small horde of Demonic Spiders tags along for good measure. Players who've managed their money poorly may very well need to restart or go back several scenarios to stand a chance.
The reason why Kirkus Zan Valfarbia isn't as bad in the last scenario of Lune Zoldark's route is because there are more Super Robot units at the player's disposal and while both routes have two pilots who can initiate "Maximum Break"note Viletta Vadim and Aya Kobayashi in Masaki's Route, Kyosuke Nanbu and Katina Tarask in Lune's route, most of the units in Masaki's route are Real Robots. Oh, and regarding Ing Egret in Masaki's route: if you think the resident Game Breaker will save you at this point in the game, think again; the Ashe and his later pilot abilities aren't available until the "EX" scenarios are over.
They Wasted a Perfectly Good Plot: A lot of dangling plot points from the previous games are just explained away in a single sentence following the Final Boss in Coffin of the End. At the same time, although players begin with Sakito Asagi, he turns into an irrelevant Decoy Protagonist once Masaki returns. In fairness, the series and the company were already dying by that point due to critical and commercial failure.
The Woobie: Tytti lost her family to a psychotic murderer who killed them right in front of her on the surface world, and although she prevents him from gaining exclusive rights and privileges in La Giasnote Initially, he was chosen to be the Herald of the Gaddeath, not Tytti, he escapes captivity from the Kingdom of Langran authorities. When she sees him again, Tytti is Brainwashed by him and relives her bad memories from the surface; to top it off, the psychopath kills a fellow Herald who's been trying to get her affections for a large part of The Lord of Elemental, thereby invoking her fear of building a new relationship with other men. OUCH...and you thought Setsuko Ohara has it bad...
Coffin of the End makes this worse for Tytti: the Elemental Lords are missing, as are the rest of the Heralds, with La Gias in ruins by an unknown antagonist. Forced to align with Shu, Tytti has no choice but to use a regular Elemental Machine.
Not really. She'll get her fellow Heralds and her Elemental Lord back (see here), we just don't know how yet.