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The Zero Exo Suit can be unlocked by beating the game, which strikingly resembles Zero from the Mega Man X series. Additionally, a giant Zero Mech can be found in Kiichiro Plaza.
Contributed by Tuli0hWut
The Jill Sandwich Exploration Trial found in Capcom Heroes, which requires Frank to eat a sandwich equipped with the Jill Valentine costume, is a reference to the infamous line said by Barry Burton in Resident Evil, in which he saves Jill from a trap and tells her that "you were almost a Jill Sandwich!"
Contributed by Tuli0hWut
Located throughout the game are a few arcade cabinets that represent Capcom arcade games:

Final Fight
1942
Street Fighter
Ghosts 'n Goblins
•Rival Schools: United by Fate
Darkstalkers
•Captain Commando
Contributed by Tuli0hWut
There are locations that include merchandise and items from other Capcom games along with some carboard cutouts of Street Fighter characters upon entering them:

•Tetro's Comics & Collectibles located in Old Town

•SuperPunch Comics located in the Willamette Memorial Megaplex

•Ja-POP! located in Kiichiro Plaza

•The Prawp Family home located in West Ridge

•King Hiro Arcade located in Kiichiro Plaza
Contributed by Tuli0hWut
There are posters that can be found only in Capcom Heroes that pay homage to several games developed by Capcom:

Dead Rising
Cadillacs and Dinosaurs
Street Fighter
Viewtiful Joe
Darkstalkers
Devil May Cry 4: Special Edition
Zack & Wiki: Quest for Barbaros' Treasure
Dino Crisis 3
Rival Schools: United by Fate
Okami
Lost Planet 3
Resident Evil VII: Biohazard
Phoenix Wright: Ace Attorney − Spirit of Justice
Super Puzzle Fighter II Turbo
Contributed by Tuli0hWut
As part of Dead Rising 4: Frank's Big Package update, Capcom Heroes became a playable mode in the game where Frank can play as characters that pay homage to other Capcom franchises. They can be unlocked as followed:

Classic Frank (Dead Rising)
Dante (Devil May Cry)
X (Mega Man X)
Ryu (Street Fighter)
Cammy (Street Fighter)
Viewtiful Joe (Viewtiful Joe)
Mecha-Zangief (Marvel Vs. Capcom)
M. Bison (Street Fighter)
Adam the Clown (Dead Rising)
Arthur (Ghosts 'n Goblins)
Bass (Mega Man)
Morrigan (Darkstalkers)
Sissel (Ghost Trick: Phantom Detective)
Zombie Frank (Frank Rising DLC)
Jill Valentine (Resident Evil 3)
Amaterasu (Okami)
Akuma (Street Fighter)

In addition, the Shadow variants are a reference to both Shadaloo experiments Shadow and Shadow Lady from the Marvel Vs. Capcom series.
Contributed by Tuli0hWut
According to Terence J. Rotolo, the series voice actor for Frank West, he was not asked by Capcom Vancouver to reprise his role for the fourth game due to Dead Rising's asset manager, Trant Lee-Aimes, changing Frank West's character development. Lee-Aimes was asked by fans regarding the lack of Rotolo's involvement within the game, to which he responded in a fan Q&A:

"We wanted to work with someone to provide a more grizzled, older take on Frank at this stage. It's no disrespect to history or previous actors--TJ Rotolo has done a bang-up job."

Rotolo shared a Change.org petition made by fans through social media to have him return back for this game, but to no avail.
Contributed by Tuli0hWut