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.
12 Characters
http://twitter.com/#!/lupinko/status/89199598131884032
http://twitter.com/#!/lupinko/status/89200503568859136
This seems to be a reference to Niitsuma; some have speculated that it is a reference to this video:
http://www.youtube.com/watch?v=MOZEaTDXFrY
Phoenix Wright
http://twitter.com/#!/lupinko/status/88424541361152000
In Japanese, this translates to Phoenix Wright's surname, "Naruhodo".
Strider Hiryu
http://twitter.com/#!/lupinko/status/88420025538580481
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.
http://twitter.com/#!/lupinko/status/89155026915831808
The top-left corner of this image has been altered; this is the original cover:
http://i.ebayimg.com/00/$%28KGrHqIOKnEE2ZvdTEJdBNvq7%28k+Cw~~_35.JPG
The silhouette that has been added to the image is without a doubt Strider Hiryu's:
http://www.freewebs.com/strider-hiryu//Strider Hiryu/strider_hiryu.jpg
This related tweet cements Master Chibi as a reliable source, which is important in later arguments:
http://twitter.com/#!/lupinko/status/89157218200600576
Vergil
http://twitter.com/#!/lupinko/status/89024544764989441
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.
http://twitter.com/#!/lupinko/status/88806044213587968
James Cromwell played Vergil in a "Dante's Inferno" film.
Gambit
http://twitter.com/#!/lupinko/status/89240411717120000
http://twitter.com/#!/lupinko/status/89238408622391296
http://www.youtube.com/watch?v=CSlMIuOEenE&playnext=1&list=PL99A5E1FFBF2742B3
http://www.youtube.com/watch?v=X9Srh6pyyFs
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:
http://en.wikipedia.org/wiki/Taylor_Kitsch
http://twitter.com/#!/lupinko/status/89155026915831808
Gambit was a Horseman of Apocalypse for a while:
http://en.wikipedia.org/wiki/File:GambitDeath.png
Apocalypse
http://twitter.com/#!/lupinko/status/89155026915831808
Apocalypse is mentioned.
http://twitter.com/#!/lupinko/status/88881487730065408
http://twitter.com/#!/lupinko/status/88881287191998464
http://twitter.com/#!/lupinko/status/88881232468910080
http://twitter.com/#!/lupinko/status/88881157466374146
http://twitter.com/#!/lupinko/status/88881101396910080
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
http://twitter.com/#!/lupinko/status/88905161216503808
Ghost Rider gets a mention.
http://twitter.com/#!/lupinko/status/89206195537199105
Possibly relevant:
http://sidcustoms.blogspot.com/2010/12/ghost-rider.html
http://twitter.com/#!/lupinko/status/89240411717120000
Hockey team "The Fernie Ghostriders" have a "Tim Hortons Player of the Week":
http://www.fernieghostriders.com/leagues/custom_page.cfm?clientID=4615&leagueID=15854&pageid=9223
Rogue
http://twitter.com/#!/lupinko/status/88900118304133120
Lenore Zahn is the voice actress for Rogue in the old X-Men TV series.
http://twitter.com/#!/lupinko/status/88624060304605184
When Rogue absorbed Ms. Marvel's powers, she also absorbed her entire psyche, permanently.
Venom
http://twitter.com/#!/lupinko/status/88525101439516672
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.
http://twitter.com/#!/lupinko/status/89220947709657088
http://twitter.com/#!/lupinko/status/89266993798193152
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:
http://www.youtube.com/watch?v=MOZEaTDXFrY
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
http://twitter.com/#!/lupinko/status/88503530771582976
In Dead Rising 2, you are able to make mixed drinks, among which are Orange Juice and Milk.
http://twitter.com/#!/lupinko/status/88503553576013824
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):
http://dead-rising.wikia.com/wiki/Nectar_(Dead_Rising_2)
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:
http://deadrising.wikia.com/wiki/Coffee_Creamer_(Dead_Rising)
Jubilee
http://twitter.com/#!/lupinko/status/88813719622123520
Jubilee is Asian. "Yellow fever" is a slang term for having a sexual appetite for Asian women:
http://www.urbandictionary.com/define.php?term=yellow+fever
http://twitter.com/#!/lupinko/status/88804888468930560
http://twitter.com/#!/lupinko/status/88804942478974976
Recently, Jubilee was bitten by a vampire, and is now one herself:
http://en.wikipedia.org/wiki/Jubilee_(comics)#Vampire_abilities
http://twitter.com/#!/lupinko/status/88868885465538560
Jubilee is mentioned again.
Roll
http://twitter.com/#!/lupinko/status/88700157037785088
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:
http://www.gamefaqs.com/boards/995375-marvel-vs-capcom-3-fate-of-two-worlds/59045947/655500347
http://twitter.com/#!/lupinko/status/88700108446760961
"Ryuusei" can mean "meteor" or "star" in English. Some have taken this as a hint toward a Starforce iteration of Roll appearing.
http://twitter.com/#!/lupinko/status/88810596581130241
http://twitter.com/#!/lupinko/status/88811838007025664
Some have taken Roll being toy-like, and a "robochick" to relate to these tweets.
Megaman Starforce
http://twitter.com/#!/lupinko/status/88481992273952768
http://twitter.com/#!/lupinko/status/88482079121219584
The Starforce series has characters called "wizards". Among those wizards is a character named Omega-Xis:
http://megaman.wikia.com/wiki/Omega-Xis
This character is specifically blue and green. When Megaman acquires new abilities in this game, he changes color.
http://twitter.com/#!/lupinko/status/88700108446760961
"Ryuusei" can mean "meteor" or "star" in English. Some have taken this as a hint toward a Starforce character appearing.
Ms. Marvel
http://twitter.com/#!/lupinko/status/88624060304605184
http://twitter.com/#!/lupinko/status/88629994527522816
http://twitter.com/#!/lupinko/status/88630071476228096
These are all lyrics from the song "To Your Beat", by M-Flo:
http://www.kiwi-musume.com/lyrics/m-flo/beatspacenine/toyourbeat.html
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:
http://media.comicvine.com/uploads/0/4/15354-2910-17111-1-ms-marvel_super.jpg
Regarding the babies comment, I will just link to this:
http://www.carolastrickland.com/comics/msmarvel/msmarvel2.html
Dr. Strange/Mysterio/Gill
Master Chibi on SRK confirmed that one of the three would be present in the game:
http://shoryuken.com/forum/index.ph...l-be-a-super-mvc3.132023/page-45#post-5529727
http://twitter.com/#!/lupinko/status/88481992273952768
http://twitter.com/#!/lupinko/status/88482079121219584
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:
http://en.wikipedia.org/wiki/Doctor_Strange
I have not seen a formal argument for Mysterio aside from him being a wizard who also wears a multi-colored outfit:
http://en.wikipedia.org/wiki/Mysterio
http://twitter.com/#!/lupinko/status/88657377108299777
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
http://twitter.com/#!/lupinko/status/88700108446760961
"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:
http://capcom.wikia.com/wiki/Batsu_Ichimonji
http://twitter.com/#!/lupinko/status/88480974983270402
http://twitter.com/#!/lupinko/status/88479637822390272
Not much to this; a reference to school. Batsu is a poor student in school.
http://twitter.com/#!/lupinko/status/88625359037276161
Some have taken this as an indication of Shoma Sawamura:
http://capcom.wikia.com/wiki/Shoma_Sawamura
Megaman X Character
http://twitter.com/#!/lupinko/status/88810736704425985
There is a relationship between the Megaman X series and Blade Runner plotlines:
http://30ninjas.com/blog/megaman-vs-rick-deckard-android-versus-replicant
Cable
http://twitter.com/#!/lupinko/status/88499767067422720
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:
http://twitter.com/#!/lupinko/status/88657377108299777
James Howlett is Wolverine's true name:
http://en.wikipedia.org/wiki/Wolverine_(comics)
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:
http://en.wikipedia.org/wiki/Legacy_Virus
In Ultimate X-Men, Cable is a future version of Wolverine; possibly relevant:
http://en.wikipedia.org/wiki/Cable_(comics)#Ultimate_Cable
http://twitter.com/#!/lupinko/status/88907927464837121
This line has been attributed to Cable; I have no source.
http://twitter.com/#!/lupinko/status/89007693485977600
http://twitter.com/#!/lupinko/status/89007734053285888
Some have taken this to be a reference to Cable, as he is from the future.