Vulcano Rosso, Zero, Megaman X, Nemesis, Fantastic 4, Thor, Jimmy Rey (as god Tier like Seth in SFIV), Devilot, Power Stone CowBoy (Accel), Donovan, Batsu, Roy, Akira, Kyosuke, The Punisher. Mega Crush, the same game with more characters.

The Sentry and Ameratsu as special boss characters since they are the most powerful beings in their own individual universes

no way too meet expectations this game needs 100 plus characters, 48 selectable playable characters and 2 bosses 1 from each universe

Marvel side - I would keep all characters from MvC2, except War Machine, I'd just make him a different armor for Iron Man instead of a different character, and I would add the following characters:

• - Beast
• - Quicksilver
• - Deadpool
• - Thor
• - Nightcrawler
• - Jean Grey/Phoenix
• - Mystique
  
• - Black Cat
• - Luke Cage
• - Spider-Woman
• - Strong Guy (this guy would be so much fun!)
  
• - Multiple Man
  
• - Iron Fist
• - Scarlet Witch
• - Doctor Strange
• - Daredevil
• - Elektra
• - Ronin
• - Kingpin
  
• - Black Tarantula
• - Carnage
• - Firestar
• - Domino
• - Blob
  
• - Ms. Marvel/Warbird
• - Black Panther
• - She-Hulk
• - Namor
• - Adam Warlock
• - Thing
• - Human Torch
• - Invisible Woman
• - Mr. Fantastic
• - Sentry
• - Blade
• - Punisher
• - Black Widow
• - Cloak & Dagger (with Dagger being the main attacker and Cloak being more of a constant helper, defender and teleporter, but who could also use his teleporting to bring in something massive like a train to run over the opponent, for example; they could also have a Super Combo in which Cloak grabs the opponent and sends her/him into his realm of darkness, where Dagger and some unseen and unidentifiable things attack the hell out of their opponent until she/he gets kicked out of Cloak's dimension, kind of like a freaky Shun Goku Satsu)
• - Wonder Man
• - Silver Surfer
• - Ghost Rider
• - Mephisto
• - Onslaught (playable, this time)
• - Apocalypse (same here, and with a smaller form as well)

And it would be cool to have a background with Dazzler performing a live show.

CAPCOM side - I'd remove Roll, Servbot and possibly, but not definitely, Tron Bonne (idk) but would keep all other CAPCOM characters, including Abyss, and I'd add:

• - Guy
• - Blanka
• - Sagat
• - Rose
• - Oro (maybe he'd have to use both arms in this one!)
• - Skullomania
• - Kairi (one of my favorites)
• - Garuda
• - Blair Dame
  
• - Area (could have Tron Bonne come in and help out?)
  
• - Demitri
• - Hsien-Ko
• - Donovan
• - Dante
• - Viewtiful Joe
• - Nemesis (I'd like to use him to mop the floor with Jill's face)
• - Alex
• - Ibuki
• - Elena
  
• - Gill
• - Q
• - Yun & Yang (it would be interesting to control both at the same time)
• - Devilotte
• - Crimson Viper (I don't particularly like her, but I think it would make sense)
• - Leo
• - Kenji
• - Tessa
• - Mai Ling
• - Hauzer (with Valdoll appearing for a Super Combo)
  
• - Akira (from Rival Schools)
• - Daigo
• - Kyosuke
• - Haggar
• - Cody
• - June (from Plasma Sword)
• - Rain (from Star Gladiator 2)
• - Zero (from Megaman X... and Megaman should be more like X than pre-X)
• - Samanosuke Akechi (from Onimusha: Warlords) or Hideyasu "Soki" Yuki (from Onimusha: Dawn of Dreams), or both
• - Frank West (he looks fun to use in Tatsunoko Vs CAPCOM)
  
• - King Arthur (but redrawn to have a decent height and stature and be less cartoony)
• - Firebrand
• - Amaterasu (from Okami)

I'm thinking if Guile or Charlie shouldn't be dropped. If it were up to me I'd drop Guile and just replace him with Remy... but that would never happen, would it? No, I don't think so. Guile's too much of a SF icon.

The ones listed in grey are secondary choices, but if in bold grey they're in between primary and secondary. The reason I did that was because the characters naturally weigh differently in terms of importance and probability of being included, and since I couldn't help but naming some of my personal favorites, that helped me make a more objective list within the bigger list and set aside some of my personal preferences. For example, I'd love to see Kairi in it more so than Zero, but Zero's inclusion just makes more sense given his popularity. Kairi was a very biased choice, and therefore I had to make it a secondary one. That's 25 to 43 characters for Marvel and 24 to 42 characters for CAPCOM (I counted pairs of characters such as Yun & Yang as one character instead of two), plus the ones kept from MvC2 from both sides, that's a total of anywhere between 100 and 138 characters. That would be fun... and somewhat scary.