Marvel vs. Capcom 2: New Age of Heroes is the fourth installment in the Marvel vs. Capcom series of tag team-based fighting games. Players select a team of three characters to compete in a one-on-one battle, as opposed to teams of two characters in the series' previous entry, Marvel vs. Capcom: Clash of Super Heroes. The game introduces a more refined version of the "Variable System" used in past Marvel vs. Capcom games, which allows players to tag in other team members at any point during the match. Unlike Clash of Super Heroes, which features unplayable partner characters that the player can summon at will, Marvel vs. Capcom 2 re-implements the "Variable Assist" gameplay mechanic introduced in Marvel Super Heroes vs. Street Fighter, allowing players to call upon one of their off-screen team members to perform a single special move to aid them. Each playable character possesses three different types of assists, denoted by the Greek letters α, β, and γ, which can range from projectile attacks to healing moves. Assist characters receive extra damage if struck by the opponent. As characters fight, the team members not in play will also slowly regenerate their life gauges. A match lasts until one team completely runs out of vitality for all three fighters; if the match timer reaches zero before either team is knocked out, the player with the most remaining health is declared the winner.
Similar to prior installments, as characters deal and receive damage, a colored meter at the bottom of the screen known as the "Hyper Combo Gauge" will gradually fill. When the meter is full, the player can use it to perform several special techniques, such as "hyper combos", powerful attacks that deal heavy damage; "delayed hyper combos", which allow the player to execute multiple hyper combos consecutively; and "variable combinations", which summon the player's entire team to use their hyper combos simultaneously. The game also introduces a new gameplay mechanic called the "snapback", which forces the opponent to switch characters. Marvel vs. Capcom 2 features a modified version of the six-button control scheme from Clash of Super Heroes. Instead of six attack buttons separated as three pairs of low, medium, and high-strength punches and kicks, the game utilizes a setup of four attack buttons and two assist buttons.