In one of her after-battle quotes, Xiaoyu quotes Lee Chaolan's infamous "excellent" quote, prompting No Just No Reactions from Jin and Heihachi.
When KOS-MOS and T-elos perform their version of Shion's Spell Blade Tech Attack as their Multi Attack, the two recites the same poem Shion says. KOS-MOS herself did this originally in Endless Frontier EXCEED
X has attacks from previous games (from Mega Man X1 up to Mega Man X4) such as Storm Tornado, Spin Wheel, Speed Burner, Tornado Fang, Triad Thunder, Frost Tower, Twin Slash, Rising Fire, Mega Man X3's Buster Upgrade Cross Charged shot, and even the Hadouken! He also gets the Ultimate Armor and its Nova Strike as part of his and Zero's Limit Break. Meanwhile, Zero uses the dash cancel exploit from X4 in one of his attacks and reverses the direction of his Kuuhazan in one of the attacks, which could be used in his original game to get in more hits and increase Zero's hangtime.
Imca mentions how to pull off a charge shot in crosshairs to X. The funny thing is, crosshairs already exist in Mega Man X7 where X can use the crosshair attack.
One of the post-battle dialogues between X and Zero is X's ending in X4 where if he becomes a Maverick in which Zero cuts him off.
At one point in the story, the party comes across the ghost of Iris which causes Zero to have a Heroic BSOD that the party must rescue him from. He even utters his infamous "What am I fighting for?!" line. (Or at least the subtitles in the English version do.)
The Tension Blaster name actually goes back even further than that. They were the name of Ulala's guns in Phantasy Star Online and they could be unlocked as weapons for the player to use. So Japanese players WOULD get the reference after all if they played that.
Many, many of her lines are taken from points in her games; the chapter she appears in is titled Ulala's Swingin' Report Show and she even calls it out like at the start of stages in her games. And during the ending, Ulala signs off with her signature "Spaaaaaaaaaace Channel 5!~" call from the end of levels in her game.
One of the characters she summons is Scooter. When summoned, Scooter runs into the enemy and blows himself up, causing his head to fly off and land on the ground, followed by another headless Scooter running in from offscreen to pick up the head, reattaching it and running away, just like in his screen-clearing attack in the original game.
In the epilogue of Namco × Capcom, Demitri mentions to Morrigan the reason why there were Q-Bees that showed up in the Infernal Village is because Jedah's coming back. Well, guess who's here in this game; also qualifies as a Brick Joke considering the former game was out 7 years ago.
Back in Namco × Capcom, you get to use both Demitri and Valkyrie at prologue 4 (at the entrance to Astaroth's castle). In this game, you get to use them at prologue 4 (sans Morrigan as she appears at prologue 5, although she was mentioned).
Tron's support attack starts off by firing her Beacon Bomb, then one of the Servbots drives the drill car, followed by Servbots throwing bombs and firing the bazooka. All of these were in The Misadventures Of Tron Bonne game. Meanwhile, she also retains her Servbot Takeout and Servbot Surprise from Marvel vs. Capcom series.
The title of Chapter 3 is even called The Further Misadventures of Tron Bonne.
And the reasoning why she's traveling? She's looking for parts to build the rocket ship that they could ride to the moon. Yeah...
Chun-Li's the very first person Reiji asks as to what the group's doing at Shibuya, making the same reference that she's the first person (aside from KOS-MOS, Shion, and M.O.M.O but they're not present) Reiji and Xiaomu meet in Namco × Capcom. That and of the four people who know them, she was the most reliable (one being a former hardcore Shipper on Deck with Reiji's Foe Yay with Saya, another a succubus, and a third a pirate from the future).
One of the online games Xiaomu plays is apparently The World.
One of Kaguya's attack animations has her using a fan to control her sword's chakrams, much like how her friend and fellow protagonist Suzuka did with her Mini-Mecha in Endless Frontier.
When Valkyrie meets up with Kurt and Riela with that whole seventeen joke, Kurt makes a reference that the number 17 of the Nameless was practically a slacker (referring to Ilmari Gasotto). Oh, and Kurt brought his candies again and even has them as one of his skills.
Pair them up with Saya and she'll state that she wants to be Number 99. While if you pair up Imca with Reiji and Xiaomu, the latter wants to be Number 765.
The "White" Arremer is a nod to an obscure ability of the Red Arremers from the first Ghosts N Goblins: they turn white, faster and more aggressive if not killed fast. This is actually the second time this ability is referenced.
Ulala mentions how Devilotte's father only gave her 300 yen when she left, just like in Cyberbots.
Late in the game you fight two Astaroths, exactly like in Ghosts N Goblins. Although to be fair, Astaroth being split into two was already in Namco × Capcom as punishment for not defeating Arthur back then.
He also mentions that some of his friends have studied Ken's fighting style via correspondence coursenote Specifically referring to Hinata, and may also be referring to Chairperson as well, though what she learned was actually Dan's Saikyou style
Arthur and Devilot used to be assists before in the first Marvel vs. Capcom - and they reprise their roles here.
Lady's Solo Attack includes some of her acrobatics seen in the opening cutscene to chapter 6 of Devil May Cry 3 where it's her against a horde of Hell Prides and Hell Lusts, namely her spinning-flips dual-wielding gun-attack. Add in one of her quotes during her Assist is "Mother, give me strength..."
In chapter 10, after Jedah enters the stage, Dante notes that the one thing he hates most is someone who talks more than he does, which is the same thing he said when he first meets Jester, also in Devil May Cry 3.
A clever one with Sanger, which doubled with Mythology Gag. When he is a Solo unit, he uses Unyo no Tachi and Daisharin in his attacks which comes from Daizengar. When he is a Rival Character, he only uses Ichimonji Giri which is the Signature Move of Wodan Ymir and his Thrudgelmir, Sanger's combat rival in SRW OG 2 who is technically his Alternate Universe version and his stand-in for his role as The Dragon in Alpha Gaiden. Also note that Ichimonji Giri is Wodan's version that is shown in the OG series, while Sanger's version from his debut in Alpha Gaiden was named Inazuma Juuryoku Otoshi.
And then he refers to "him" mentioning Endless Frontier to Sanger. The only two people who would tell someone that would either be Axel or Kouta and Kouta's already keeping quiet about his adventures (so as not to confuse people), while Axel currently is with the Kurogane crew training Touma Kanou
Pair up Valkyrie with Reiji and Xiaomu and both Valkyrie and Xiaomu make references in a game when the two of them were together called Brave Company, in which Reiji (who didn't show up) has no idea what they're saying.
The Rainbow Bridge Valkyrie put up in Namco × Capcom gets referenced again when Kaguya powers up the treasure at Kagura Amahara to erect one. Over to where Valkyrie is at.
Speaking of Kaguya, Saya's cow flunky still has a crush on her.
Pair up Haken and Kaguya with Ulala and Kaguya will mention Neige and Suzuka while Haken will mention Aschen and Aledy.
Pair up KOS-MOS and T-elos with Sanger and the latter outright name drops Shadow Mirror and accuses both the robots to be part of that world. T-elos has no idea what Shadow Mirror is, while KOS-MOS, who does know that Haken is W00, assures Sanger that they're not part of Shadow Mirror.
If you pair up Kurt and Riela with Sanger, Sanger thinks that he and the Nameless aren't so different from each other (referring to him and the Kurogane crew protecting the Earth in the shadows because they're technically still traitors to the Earth Federation Alliance after siding with Bian Zoldark and the Divine Crusaders). While if you pair them up with Bruno, the latter has bad memories being led by soldiers (since in his game, his superiors were killed by spies).
Chun-Li and the others who show up in Shibuya still refers to the city as a closed city (which also includes the Akihabara district) due to the problems with dimensional rifts perpetrated by Ouma agents because Shinra hasn't resolved it yet.
Yuri remarks how nothing ever good happened to him in a desert.
While on board The TarqaronDante remarks how he and towers have a bad history. Lady, in later chapter, also have the same feelings.
Put Saya with Yuri and Estelle and the vixen will bring say how Estelle isn't an "enchanted belle" yet, much to Estelle's chagrin, to which Yuri brings up how that's a title Estelle can acquire when she gets her outfit during the seduction incident.
Likewise, if you pair them up with Neneko, she tells Estelle to transform into another outfit, causing her to reply that she'll turn into a Massage Therapist, yet another one of her costume titles. Again, Yuri isn't pleased and wishes she'd actually pick one with some battle ability.
Jill tells Chris to shut up when he tells Jill that she's almost a Jill sandwichnote The line was not said, but Jill knows what he's about to say, which is a line said by Barry in the first Resident Evil after the team gets into the abandoned mansion at the Arklay Mountains and Jill barely manages to avoid being squashed by a Descending Ceiling trap.
The attack moves used by Chris and Jill are taken from Marvel vs Capcom 2 and 3, and Resident Evil: 5 and Revelations.
Jill's Database entry refers to her as the Master of Unlocking, a title given to her by Barry in the first Resident Evil.
Dante mentions that Valkyrie is alone in his office without her companions traveling with her. They consist of Clino Sandra and Sabine, two characters in the Valkyrie no Bōken series who were playable in Namco × Capcom.
In one of Hsien-ko's battle quotes, she says that it's not the time to be saying "aiya" or "xie xie" anymore; which is the exact same thing she told Fong Ling in Namco × Capcom when enemies were attacking the Spencer Lane.
Also in that same pre-battle conversation, Frank says that it's also not the time to say "good" or "fantastic!" which are quotes he uses in Dead Rising depending on how good the photos you take are.
Hsien-ko's presence on the Bermuda is also a continuity reference since she starts out fighting on the Spencer Lane's outer deck in Namco × Capcom.
There are three moments in the game when the Sakura Wars trust increase chime plays. First is in Ch. 9 when Ogami compliments Erica for her contributions to the Imperial Assault Force. The second moment is in Ch. 25 when Ogami and Sakura save the Fujisakura from being overflowed with spiritual energy and Ogami assures Kaguya that the tree will not die. The third moment is during the epilogue when Ogami thanks Aura for helping them get back to their homeworlds. Every time this happens, Sakura shows her Clingy Jealous Girl tendencies.
Paring anyone whose a princess with Flynn will result in Flynn making a quick little speech about how he will be a knight and protect them, something that he both does in game, and in the various spinoff titles in the Tales of franchise.
When Yuri meets Sanger, Sanger challenges him to a fight making Yuri sarcastically comment that "Is it a rule that everyone with a big sword has to be like this?" which reflects people he's met like Clint.
Also when Estelle comments that they should talk this out, Yuri says he is, which references how he and Flynn dealt with their differences.
When Yuri discusses Vile, he compares him to Zagi.