Marvel vs. Capcom 3 and Ultimate Marvel vs. Capcom 3 featured more of my direct design decisions than any other games outside of Marvel Pinball, and they were also some of the most well received. Among the highlights: 

Level Design and Fan Service

For UMvC3, Capcom doubled the number of stages by creating second versions of environments that already existed (changing day to night, adding some new angles and lighting touches, etc.). I proactively approached them about better representing the Marvel brand than they had originally planned to do with the new interpretations of the Hand ninja and Metro City stages.

• Shadowland: The original pitch for a new Hand ninja stage made no new references to Marvel lore, which felt like a wasted opportunity for fan service. I proposed that they instead make the stage more relevant to the Marvel mythos by creating a theme based on the then-recent "Shadowland" story arc, in which the Hand was firmly established in the heart of Manhattan -- pagoda, evil Daredevil and all. They were able to build almost the entire level without needing to create many new assets, of which there were very few. 
• Days of Future Past: Changing Metro City -- a Capcom location -- to a level based on the X-Men story "Days of Future Past" was a tougher sell, since it shifted the balance of stages to be mostly Marvel based. But they went for it anyway, and it became one of the most talked-about stages. Part of that was re-creating the iconic poster from X-Men comics, for which I suggested using characters from Marvel vs. Capcom 2 who were not in UMvC3 (including characters like Cyclops and Colossus being placed exactly where they were on the original poster, but with their MvC2 designs). Oh, and internet, if you were holding out hope that Mega Man was playable because he wasn't "SLAIN" or "APPREHENDED"...you can blame me. I'm the one who suggested he get no designation -- pretty much just because I like the guy -- and they went with it. 

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Costume Selections

I requested that alternate skins for characters should represent influence from comics, not just be random colors (as with past MvC games). This resulted in a series of popular blog entries spanning from Marvel.com to IGN and GameSpot (plus tons of pickup from fan sites). 

Character Dialogue

Frank Tieri deserves tons of credit for all the great writing he did for both games, and I was able to add some lines for Marvel characters as well. Some have become bona fide fan favorites, like these from Deadpool: "Magneto! Welcome to die!" (itself a classic gaming reference),"Bang! Bang! Bang!", and the two Turn Off the Dark references he speaks to Spider-Man. 

Other Miscellaneous Fan Service

TONS of research went into making these games as "Marvel-icious" as possible, and it's been nice to see it recognized in articles like this one, as well as to simply hear fans celebrate just how much Marvel stuff there is in there. Below are the items in the game there because I suggested them, and I contributed greatly to the inclusions of 25, 17, 10, 3 and 1.