The Gunleon is a repair-based mecha the Wounded Lion Sphere decided to manifest in, rather than a person or a combat-based mecha to avoid fighting. It would have worked too, if Mel hadn't been killed by Breakers.
Tifa Adill and Eureka quickly become best friends, and Tifa ocasionally gives her ominous warnings about her visions of Eureka from the future. Garrod Ran and Renton Thurston form a Bash Brothers style friendship as well, and Garrod even gives Renton tips on how to handle a Mysterious Waif girlfriend. Although this gets more screentime on Rand Travis' route, it's present in both routes.
The other prominent cross-series friendship that gets more screentime on Setsuko Ohara's route is Kamille Bidan and Shinn Asuka. Like Garrod and Renton, they also become Bash Brothers, but Z actually points out the differences between them (since the fandom likes to belive Shinn is a Kamille Expy; both are quite different, as specifically pointed out by Amuro and Char Aznable). Kamille plays The Heart, The Smart Guy and is considerate of others' emotions and is saddened and angered by the warfare (his Character Development in Zeta Gundam and Z take him in a positive direction), whereas Shinn's the Blood Knight and The Berserker who views everything as his enemy (Amuro even admitted to Char that sensing Shinn's malice when he blocked him from going on a murderous rampage scared the crap out of him). Shinn's Character Development in Gundam SEED Destiny was taken in a negative direction, and he only got worse as the show went on. While Z still has Shinn go down the drain for a while, the game doesn't take him to the same extreme that the anime did, and it begins rebuilding him as a heroic figure, which truly shows on the ZEUTH route, where he never abandons the party and goes up against Gilbert Durandal.
The dimensions merged as a result of the Space/Time Oscillation Bomb are as follows:
The cross-series friendship continues in Hakai-hen, One of which is Heero Yuy and Setsuna F. Seiei, with the most prominent scene being the one after the stage Heero self-detonates the Wing Gundam. As he's recovering, most of the Wing, 00 and Code Geass cast are there to see how he's doing, with Setsuna proclaiming "You are also Gundam".
Movie-Renton addresses Gainer Sanga as "Gainer-san" and Sara Kodama laughs at him for it. This refers back to anime-Renton in Z calling him "Gainer nii-san", which is akin to "Big Brother Gainer".
Lockon Stratos tells Setsuna that if there's someone who knows how to be Gundam, it's Amuro. In one of the final scenarios where they meet Amuro, Setsuna asks him a few questions about that.
Emperor Zuul knows quite a lot about ZEXIS, due to the amount of battles quotes he has when fighting against most of the non-voiced protagonists. He even mentions a few specific things other villains don't normally know. HOW he knows all this is another question entirely.
Tengen Toppa Gurren Lagann uses an original story (Banpresto didn't use the TV or the movies: the original director made a new story just for this game). In Scenario 54, Gurren Lagann ends with Simon rescuing Nia from the Anti-Spiral's unit called "Anti-Gurren Lagann". Arc Gurren Lagann only appears as a final attack for Gurren Lagann.
Kamille pretty much acts as a mentor for Setsuna during those trippy scenes where the 00 Gundam allows him to sense the feelings of the battlefield.
Apparently Heero is the only non-Code Geass protagonist to know Zero's true identity is Lelouch Lamperouge before the big reveal. In Scenario 38 where Jeremiah Gottwald returns, Heero and the Wing Zero is the only unit that tags along with the Code Geass characters while everyone else, including all the Gundam Wing characters, go to the Dark Continent.
Saji is the 2nd person that came closest to learning the Lelouch is Zero thanks to his job at a pizza delivery and C.C., but never actively got anything concrete.
The Kedora event from Shin Mazinger traps every ZEXIS member in their dreams, not just Baron Ashura and Kouji Kabuto. That's why you see various events from each respective series.
Like the Protodevlin, Dimensional Beasts are affected by Basara's singing, damaging them in the process. Likewise, the Vajra are demoralized by Basara's songs. Basara's sound disrupts Grace's control hence why he does damage to her. For Gaioh, Basara is hitting him with life energy, which is probably something a being controlling dimensional energies doesn't particularly like when it comes to battle even if he likes it.
Kallen Kozuki gets a lot of interaction with the Gundam 00 cast. Not only does she visit Saji Crossroad in his cell on the Ptolemios, she gradually gets it into his thick skull about the world situation. Notably, when he repeatedly calls her out as a terrorist, Kallen doesn't accepts the accusation. Later, she's also responsible for motivating Sumeragi Li Noriega to return, rather than Setsuna, as he promptly leaves her with Kallen, who he thinks can talk to her better because "they're both women". While Kallen believes this is the dumbest thing she's ever heard, she manages to convince her when she tells Sumeragi the story of her mother.
In one of the route splits mid-game, ZEXIS is watching Ranka's concert. Setsuna and Heero are talking about the power of Ranka's song, but Lacus Clyne corrects them and explains her song is not about power but rather a feeling. Unfortunately, both are slightly confused:
Setsuna: "Do you know what she's saying?" Heero: "Not in the slightest."
Saisei-hen ties in Charles zi Britannia and C.C. to the plot by making the Code be a mark of the Black Knowledge. After Charles dies in the Sword of Akasha, Lelouch and C.C. discover the ultimate end of the universe, with the former at least trying to think of a way to avert it.
Also, the power of Geass is revealed to share the same roots as the Overmen of Armored Trooper VOTOMS: an ability that exists so that humans may protect themselves from Ba'al.
The Abyss is a rupture in the dimensional boundary line that connects the various worlds. It only opens at specific times and conditions, but allows safe passage between worlds with correct timing. The Eternal is able to use it to travel to the world of ZEXIS on instructions from Gen Fudou, who appears to be the only person capable of moving between worlds at will. The Abyss is also responsible for triggering the Anti-Spiral's Human Extinction System. Because the Abyss is currently acting as a conduit between the worlds of ZEUTH and ZEXIS, the system calculates both worlds' human populations together. With a combined total exceeding ten billion, it initiates the second phase.
Every person with access to the Black Knowledge is trying in their own way to resist fate. Dr. Hell wants to conquer the world so he can use all of Earth's means to fight against it. Wiseman wants humanity to evolve through conflict in order to fight the Ba'al and, failing that, for Chirico to inherit his powers and knowledge to fight in his stead. Lord Genome knows that the Spiral Nemesis is part of the Ba'al, thus works with the Anti-Spiral to suppress all Spiral beings. Charles and V.V. aim to convert all of humanity into a single consciousness so they can survive it.
It appears the Zero System was also part of Aeolia Schenberg's plans. This implies the system was designed over 200 years ago along with VEDA. In a way, this sort of appears to be a Homage to the Isaac AsimovFoundation trilogy, where the Zero System functions as the "Second Foundation" or backup for VEDA should the plan ever get derailed.
Kira has unique battle dialogue (while attacking and evading, possibly taking damage, too) when fighting Gino Weinberg and Brera Stern, where he refers to them by name; Gino returns the favor (instead, he refers to Kira by his full name). All three characters are voiced by Soichiro Hoshi.
Mikhail Blanc doesn't think Lyle Dylandy is fit to take the place of Lockon since he isn't a dedicated sniper, even more so since Mikhail took it upon himself to pick up the slack after Neil dies. Following the mission where Mikhail, Gain and Lyle needed to snipe a Dimensional Beast, Lyle comes through perfectly and he decides he's fit to take over, after all.
The demise of Nena Trinity in Saisei-hen can be on different missions, depending on whether or not you chose to trust Zero. If you chose to, she is killed in Mission 51; if not, Mission 52. What makes her death different than the anime is that Setsuna wonders what she's doing here (in the anime, the appearance of the Throne Drei was a surprise), everybody sees her kill Wang Liu Mei as Nena announced the real relationship between her and Hong Long (which, in the anime, nobody ever found out about), and that the dialogue for her death is slightly different, as Louise tells Nena she knew that she didn't want to die this way AFTER dealing the lethal blow, while Nena is coughing up blood.