First, consider this entire post to be spoilers.
I am going to do my best here to put together a summary of what has been shared by Lupinko thus far, and what able-minded individuals have interpreted the hints to be; these are interpretations, they are not categorical declarations - many are even contradictory. I will not be putting the characters in any particular order, just the arguments for them, as well as what else we have received. I will keep things as basic as possible so anyone can follow what is happening.
None of these discoveries are my own; I apologize, but it would take far too much effort to track down who initially made what connections, and this is enough work as it is. My goal is to make the exploration of these riddles more structured. People keep making discoveries, and then they fade away. We are on the right track one moment, and then off in another direction entirely. So, let's try to make progress. Everything Lupinko has said is not contained within this thread, just those things that have been said and have had some reasonable meaning put to them. If I made a mistake, or missed something important, help me out rather than berate me, and I'll add it for a future update.
This seems to be a reference to Niitsuma; some have speculated that it is a reference to this video:
In Japanese, this translates to Phoenix Wright's surname, "Naruhodo".
Clockw0rk is a renown MvC2 veteran who specialized in using Strider Hiryu. The other members of his team, Dr. Doom and Sentinel, are already in the game.
The top-left corner of this image has been altered; this is the original cover:
The silhouette that has been added to the image is without a doubt Strider Hiryu's:
This related tweet cements Master Chibi as a reliable source, which is important in later arguments:
Vergil is mentioned specifically. The "twins" mention is possible a reference to he and Dante being twin brothers, yet polar opposites, much as Danny DeVito and Arnold were in the film.
James Cromwell played Vergil in a "Dante's Inferno" film.
The argument of their association: Pokemon made collecting cards more popular than ever. Gambit throws cards. Hockey players use sticks. Gambit uses a bo staff, a type of stick. The actor who played Gambit in the X-Men Origins: Wolverine movie, Taylor Kitsch, is Canadian:
Gambit was a Horseman of Apocalypse for a while:
Apocalypse is mentioned.
These, or iterations of them, are all apparently Apocalypse quotes. I lost track of the video source - feel free to post it for reference when I update everything next.
Ghost Rider gets a mention.
Hockey team "The Fernie Ghostriders" have a "Tim Hortons Player of the Week":
Lenore Zahn is the voice actress for Rogue in the old X-Men TV series.
When Rogue absorbed Ms. Marvel's powers, she also absorbed her entire psyche, permanently.
The only thing said here is that Sandman is not to be relied upon. At the least, this is a disconfirmation of Sandman. Some have taken this as a hint toward Venom. In the Spider-man 3 film, three villains are present: Green Goblin, Venom, and Sandman. Venom (Eddie Brock) asks Sandman to join with him to defeat Spider-man in the film, but they fail. The Green Goblin joins forces with Spider-man in the film.
In Pokemon, the character Brock makes a lot of rice balls, but this was translated as "jelly-filled donuts" in the English version. Lupinko also linked to Niitsuma's infamous donut-eating video:
The argument seems to be that this is hinting at the donut/riceball/Brock relationship, and thus we will have Eddie Brock, AKA Venom, in the game.
Frank West/Chuck Greene
In Dead Rising 2, you are able to make mixed drinks, among which are Orange Juice and Milk.
Lupinko clearly intended for the result of the mixed drinks to be an accurate reference to the game (it is not, as Orange Juice and Milk make Nectar, which attracts queens to Chuck):
It has also been noted that in Dead Rising 1, the Coffee Creamer item looked much like a jug of chocolate milk; this may be relevant:
Jubilee is Asian. "Yellow fever" is a slang term for having a sexual appetite for Asian women:
Recently, Jubilee was bitten by a vampire, and is now one herself:
Jubilee is mentioned again.
Roll is always helping around the lab in the original Megaman games.
The voice actress for Roll in Tatsunoko vs. Capcom, Hiromi Igarashi, was recently seen at an event with Niitsuma:
"Ryuusei" can mean "meteor" or "star" in English. Some have taken this as a hint toward a Starforce iteration of Roll appearing.
Some have taken Roll being toy-like, and a "robochick" to relate to these tweets.
The Starforce series has characters called "wizards". Among those wizards is a character named Omega-Xis:
This character is specifically blue and green. When Megaman acquires new abilities in this game, he changes color.
"Ryuusei" can mean "meteor" or "star" in English. Some have taken this as a hint toward a Starforce character appearing.
These are all lyrics from the song "To Your Beat", by M-Flo:
When Rogue absorbs Ms. Marvel's powers, she also accidentally permanently absorbs her psyche. The line could be a hint toward Rogue, or instead toward Ms. Marvel, due to the "you" in the line. Some have taken these lyrics as a hint toward Cammy, as Kylie Minogue played her in the Street Fighter movie.
Shining star in heart; this is Ms. Marvel's original uniform:
Regarding the babies comment, I will just link to this:
Master Chibi on SRK confirmed that one of the three would be present in the game:
Some interpret these hints to be toward Dr. Strange, as he wears a many-colored robe, performs "wizardry", and his spells often look like amorphous jello:
I have not seen a formal argument for Mysterio aside from him being a wizard who also wears a multi-colored outfit:
Aegis Reflector is a move of Urien's in Street Fighter III. Gill is the brother of Urien; some people believe there to be a connection here.
Rival School Character
"Ryuusei" can mean "meteor" or "star" in English. It is part of the name of one of Batsu's signature attacks in Rival Schools, the "Shooting Star Kick"; Batsu was also present in Tatsunoko vs. Capcom:
Not much to this; a reference to school. Batsu is a poor student in school.
Some have taken this as an indication of Shoma Sawamura:
Megaman X Character
There is a relationship between the Megaman X series and Blade Runner plotlines:
This bears mention because the tweet confused a lot of people. Without Chibi's assistance, people likely never would have understood it. At first the message was incoherent, because Lupinko said the wrong name:
James Howlett is Wolverine's true name:
In the X-Men series, Cable gives Wolverine the Legacy Virus so his healing factor will develop antibodies that can be used to stop the outbreak from happening; hence, it would have been nice if Cable would have done this for AIDS:
In Ultimate X-Men, Cable is a future version of Wolverine; possibly relevant:
This line has been attributed to Cable; I have no source.
Some have taken this to be a reference to Cable, as he is from the future.