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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Common Knowledge: Many believe that the Marvel vs. Capcom games are Fake Crossovers, but on the contrary, Marvel acknowledged the continuity of these crossovers (alongside X-Men: Children of the Atom and Marvel Super Heroes) enough to assign them to their own official Marvel universe called "Earth-96169."
Strider Hiryu. Capcom's poll for best character of the Marvel vs. Capcom and Street Fighter games has him in third place, only surpassed by Mega Man and Poison. He's been in only a handful of games, a short and relatively unremarkable manga, and nothing else, getting something of 4% of the votes. This might not sound like much, but since there's 111 different voting options and most everyone with 3% or 4% have appeared much more frequently and are more mainstream. This probably has to do with his appearances in the previous Marvel vs. Capcom games, where he was one of the favorite characters of many a fan.
Fan demand was the factor in Capcom deciding to strike another deal with Moto Kikaku over his copyright status to get Hiryu into Ultimate MvC3 after he skipped out on the vanilla edition.
To a lesser extent, Ruby Heart and Amingo from 2 were popular enough to merit a few cameos over the years. Not bad, all things considering.
Shuma-Gorath, oddly enough. A surprising amount of people were happy to see him return (even if it is as DLC).
Psylocke, Gambit, and Venom are recurring mentions on polls for characters fan want to see in MvC3, almost always (if not always) ranking in the Top 5. For more details, see the respective YMMV pages for X-Men: CotA, XvsSF, and MvC1.