In the first scenario, Jin exclaims "Major Graham Aker made his career by winning battles on the field". This is the same quote a Principality of Zeon grunt says about Char Aznable in the first episode of Mobile Suit Gundam. In Scenario 9, Mike will yell "Aaaaah! Bro, a brand new weapon from the Federation military!", another line shouted by a Zeon soldier who came to Earth for the first time in the TV series.
Athrun Zala, as his alias "Alex Dino", uses the quote "Members of congress, I'd like you to accept my apologies for being rude." Quattro Bagina, who is really Char, uses these exact words in Mobile Suit Zeta Gundam, when he calls the Earth Federation Assembly in Dakar.
At the start of Scenario 12, Shinjiro Sakomizu mentions the name "Garou Ran" to Kaidou, who wonders if he's talking about a a certain Gundam pilot. The actual Garou Ran is part of a savage tribe located in BystonWell. Later, when Asap Suzuki uses the Nanajin, he exclaims "It...moves?", the exact words used by Amuro Ray when he moved the RX-78-2 Gundam for the first time. Incidentally, Yoshiyuki Tomino is the director of The Wings of Rean and Mobile Suit Gundam.
Shou Zama uses another of Amuro's quotes during Scenario 16, "There's nothing happier than this...", which is Amuro's last line of dialogue from Mobile Suit Gundam
Scenario 17 of the Europe Route has Yuuki quote "That's where people feel it as their second birthplace, give birth to children and raise them", derived from the opening narration of Mobile Suit Gundam.
Shinn punches Kazuki in the face for running away, very much in the same way Athrun did the same to him back in SEED Destiny. The difference is that it actually works here instead of making things worse.
Athrun's intrusion to the Earth Federation's meeting in Stage 22 is one massive homage to Quattro Bajeena, complete with shades, alias and his speech.
In Scenario 26, Cao Cao Gundam says "This guy, ha ha ha.". This is his character's introductory quote from the official website of the BB Senshi Sangokuden manga.
During Scenario 36, Hazard Pasha wonders "Hmm? I thought that was a woman... But, it's a man." when Alto Saotome is dressed in drag, a reference to Jerid Messa insulting Kamille Bidan in Mobile Suit Zeta Gundam when they first meet.
Despite Lacus Clyne being absent in UX, Kira states "I think it's okay to cry" and "Because people cry...", previously said by Lacus in the Mobile Suit Gundam SEED TV series. Similarly, Athrun uses the last line of dialogue from Cagalli Yula Atha in the TV series, "Don't run! Living is same as fighting!"
In chapter 42 battle, Lu Bu knocks Liu Bei into the ocean like Cao Cao did in the anime, and then Liu Bei re-emerges as the Shouretsutei once more.
In Scenario 43 of the Tatsujima Island Route, Kunio Ishigami states "Saying shut up you with a sword that looks like a saw", a quote used by Cao Cao Gundam in BB Senshi Sangokuden.
The Red Nanajin is also faster and more powerful, which is a reference to anything red being this, per by Char Aznable's legacy of the original Gundam.
Lyrics
In Scenario 12, Soushi uses quotes from the opening and ending song lyrics of Fafner in the Azure: Dead Aggressornote "Hajimareba, izure owaru" for the opening song, "Kizu wo outte demo habataki taito, sou negau no nara" for the ending song. Later in Scenario 25, Tsubaki will use another quote from another Fafner ending song "Seperation" note "Atashi, ika nakucha". Lyrics from Fafner In The Azure: Heaven and Earth are quoted by Shou in Scenario 29 note "If dead people return to the soil, then all of us, then we are all living above dead in a way", while Ryuubi Gundam or Chousen Qubeley quotes the main song lyrics in Scenario 47 note "Tamashii wa, katachi wo koe nakara...".
During Scenario 43 of the Union Route, Fei-Yen HD, Sheryl Nome and Ranka Lee will sing the lyrics of the opening song "Tori no Uta" from Dancougar Nova together note Fei-Yen - "Hokori to ai ga kyoumeishite... Kanadeteru, melody!"; Sheryl - "Tsubasa wa, kaze ni notte...!"; Ranka - "Oo sora ni inoru, Tori no Uta...!".
At one point in UX, Aira uses the lyrics from "Proud", an in-anime song from Linebarrels of Ironnote "Hitomi no naka ni utsushi dasareta kibou no kakera. Toki wo koe... Kizuna wo egaku, mirai.".
Shou uses the lyrics to "Fly Dunbine", the opening song to Aura Battler Dunbine, in Scenario 46 note "Osoreruna, kanashimuna. Shinjiru kokoro ga... Seigi ni narundaaa!".
Anime/Manga
The dialogue of Deus Ex Machina, the Linebarrels of Iron final boss, heavily imply that he has memories of his counterpart from "Flowers of Steel", the precursor to the original series.
West will use the catchphrase of Basara Nekki as "Today's stage is a full house. Galaxy listen to my song, that is! Love heart to you!", combined with his line of dialogue from the Demonbane visual novel, in Scenario 43 of the Union Route. Finally, during Scenario 51, West quotes "Step on the pedal and join together the timing...", a reference to the Shine Spark attack of the Getter Robo G.
During the ending, Zhang Fei Gundam says "I see, there is the possibility of Zhuge Liang saying "Hawawa~.", a reference to the Zhuge Liang character and her catchphrase in Koihime†Musou. Zhuge Liang's response is also a refence to Mitsuteru Yokoyama's version of Romance of the Three Kingdoms.
If you manage to save Mamoru, after he reappeared in Stage 41 he'll yell a line quoted directly from Kamen Rider Spirits; and after the scenerio, the group will discuss who should pilot the Mark Funf (since Hiroto is now its pilot), and Yamashita suggests that they can make another unit so that both can fight as Goubain Z and Great Goubain. Of course it doesn't stick.
The Nanajin changes colors inexplicably from green to red. This mirrors how the Billbine changed colors from red to green amidst the Climactic Battle Resurrection in its series's climax.
Miscellaneous
Doc. West's Destroyer Robo has S Rank Terrain in Water for a Bonus. This is because in the Visual Novel, when Doc. West calls it from the ocean, it was rusted and could not fight.
Demonbane's Bonus is a barrier, referencing its Elder Sign barrier from the visual novel, which was never used in the anime adaptation.
Richard calls Leica "the avatar of the king of angels" in Stage 3. This may seem random, until you realize that Leica was the Henshin Hero "Metatron" in the original visual novel, a plot point that was Adapted Out in the anime. Also, during the lantern scene in Stage 29, Leica will mention the name of Ryuuga (her brother who's also Sandalphon, the arch nemesis of Metatron).
In Scenario 10, Yamashita will mutter "Speaking of Koumei's (Zhuge Liang) traps...", which is what a strategist says, who was intimidated by Liang's resourcefulness, to a subordinate in Romance of the Three Kingdoms. "Koumei's trap" is also a famous meme in Japan.
In stage 17, Mikhail Blanc says "Main point everyone, why are you trying to split my glasses at every opportunity!?". This is a reference to his Heroic Sacrifice in the original, and his memetic status gained in Super Robot Wars L.* In short, due to an in-game bug, excessive use of Mikhail will make him permanmently unsaveable; doesn't help that many fans will sacrifice him on purpose in order to get Loli!Klan on his VF-25 In the same vein, Kaidou says "Whatever the reason may be, this is a chance to crush that bastard!", a reference to quote by Super Robot Wars K protagonist Mist Rex, though in this context it works much better.
Like with Wufei in L, Katou Organization recruited another proud Chinese warrior infamous for being a turncoat (but for different reasons) in Lu Bu, who is based on the Tallgeese III, an Endless Waltz mobile suit and successor to the Tallgeese II piloted by Treize Khushrenada whom Wufei killed. If the player is on the Japan Route of the first route split, Lu Bu is also fought in the scenario where Soubi first appears, whose villainous anime version in L is close enough with Wufei that the latter is among those needed to persuade the former to join as a secret unit despite being from different series.
