Richard Krueger calls Joey Jones "Jojo" at one point. Besides referencing Joey's name, Richard is voiced by Jurota Kosugi, who also voiced Jotaro "Jojo" Kujo in the popular Star Crusaders OVA. In another Shout-Out to JoJo's Bizarre Adventure (specifically Jonathan Joestar from the "Phantom Blood" arc), during Scenario 14 of the American Route, Richard says "Guten morning, Mushu Daijuuji. And Joestar" and "It's like a reunion joke, isn't that right, Jonathan?"
Agnes Berge is voiced by Chihiro Suzuki. When attacking with the Riot B's Proton Saber (Maximum Output), the machine takes a combat stance similar to Luke von Fabre, during one of his hidden Secret Artes. Additionally, Agnes sounds just like Luke during the earlier parts of the game, then deepens his voice significantly in later scenarios, making him sound more like Asch.
In Scenario 15 of the America Route, Soushi will state "With movement like a pendulum, barrage of accurate strikes...That technique just now, almost like boxing!", a reference to Ippo Makunouchi. Both characters are voiced Kohei Kiyasu.
In Scenario 16 of the Japan Route, Joe Maya will exclaim that "he has no name to give to fiends", a reference to Rom Stol. Joe and Rom are voiced by Kazuhiko Inoue.
At one point in UX, Lunamaria Hawke says "That's right: things go like this. When you yourself want it to be this way from how your heart feels when the natural time comes, you follow those feelings." These are the words Maaya Sakamoto, who voices Lunamaria, commented on during her wedding.
Reny, voiced by Noriko Hidaka, will exclaim in a save-quit dialogue "Sky Demon clad in flame is undefeatable!", which is what Noriko Takaya says in her home series. Furthermore, "I decline Space Monsters!" is a reference to the "Uchuu Kaiyuu" ("Space Terrible Monster Crowd") of GunBuster
In the ending, Johnny's quote "According to Monthly Men's Hobbies... Essayist and modeler jobs are being done recently." is a reference to Haruna Ikezawa and her hobbies, which includes writing for multiple magazine serializations. Interestingly, being a hardcore modeler became a topic in the Hobby Japan magazine.
Aoi punches Augustus with Absolute Nova Beast for a finish, like she punched Moon Will in the Dancouga Nova anime. Moon Will and Augustus are voiced by Norio Wakamoto. Also serves as a double Mythology Gag of characters voiced by Norio Wakamoto being punched to defeat, and Wakamoto characters being defeated by people from Dancouga (since he also voiced Shapiro Keats in the original series).
Mileina says she loves Tieria, which was in the movie itself too. In Shinkyoku Soukai Polyphonica Corti and Phoron were suspected to be lovers; Mileina and Corti are voiced by Haruka Tomatsu and Tieria and Phoron by Hiroshi Kamiya.
Graham expresses desire to embrace crossdressing Alto. They're both voiced by Yuuichi Nakamura.
Both Graham and Moritsugu are non-main character Ace pilots. Voiced by Yuuichi Nakamura too.
Irony as She Is Cast: During the saving skits, Fei-Yen HD (aka Miku) starts to speaks in a very robotic way, contrasting with her cheerful personality during the game. This is mostly her voice actress trying to sound like Miku just like in the original Vocaloid software, rather than Banpresto trying to use the software for that job. Ironically, she does a bad job doing that, even if that scene is supposed to be a Tear Jerker for the player.
Gundam SEED Destiny characters are pretty much integrated into the Fafner cast, with Shinn Asuka and Lunamaria Hawke helping them battle the Festum after their war ended (Cagalli Yula Athla is their sponsor; this implies Shinn has made some peace with ORB).
Team D has retired, yet received Laser-Guided Amnesia and went back to their ordinary lives, leaving only Eida and the R-Daigun for a good chunk of the game.
BB Senshi Sangokuden is another "just there to support the other plots" series, since they had already shown Sun Quan Gundam, Liu Bei Gundam and Cao Cao Gundam's final battle (or the middle of it) in the UX prologue. Yet Lu Bu was conveniently Back from the Dead despite he was killed way before the finale.
UX explicitly happens post-Dunbine, to which the original series was a Kill 'em All ending.