Endless Frontier features multiple worlds with combat taking place on foot. Aside from the playable characters in the game, mecha, many of them similar to the ones from the Original Generation games, are controllable by the player's actions and issuing of commands. The battle system is similar to that of Namco X Capcom (another game developed by Monolith Soft), in that attack commands during battle are issued via timed button presses, rather than through the menu system typical of the role-playing genre. The player can chain these attacks together to execute long attack combinations while issuing a new set of commands, such as support from characters on standby. The mecha featured in this game are much smaller than the ones in the Super Robot Wars series, appearing around human-size.
The game also features several characters from other series, mainly Namco x Capcom and Xenosaga. Mugen no Frontier's theme song "Butterfly" is performed by Japanese girl-group Perfume and is featured on their latest album Game.
Like its Japanese import, Atlus USA has stated gamers who have a copy of Super Robot Taisen: Original Generation or Super Robot Taisen: Original Generation 2 for the Game Boy Advance can obtain items in the localized version of Endless Frontier by inserting the game cartridge into the DS' SLOT 2 upon starting a new game.