Alpha 3 continues to use the Squad System from 2nd Super Robot Wars Alpha, where a maximum of four units can be assigned to a squad that counts as a single unit. Since all playable mecha are of different sizes, a size limit is placed, thus the player must consider building an effective squad. The system has received several improvements, including:
The ability to auto-generate squads based on "balance" (generally grouping units together by series), "power" (a strong squad leader combined with strong supporting allies), or "speed" (based on movement rate; units with the same rate are grouped together). This can be useful for the novice player or one who does not wish to go to the extra effort of building squads by oneself.
Access to the item, upgrade and pilot menus from the squad-setup menu.
The option to change each squad members' reactions when targeted by an enemy ALL attack (a choice between "dodge" or "defend")
Squad attack animation is slightly improved; the entire squad is now shown onscreen, instead of the one attacking.
Alpha 3 also contains the following:
Over 60 stages, as well as bonus "EX" scenarios, side stories to the main game.
Kazuma Kaneko, known primarily as the artist of Atlus' Shin Megami Tensei series, participates as a mechanical designer for the game. Among his designs is the Werkbau, one of the protagonist machines.
Three possible endings: the "normal" and "good" endings, with the addition of a few bonuses in the "good" ending, and the "Ideon" ending, based on the apocalyptic conclusion to the anime of the same name.
Ichirou Mizuki, who is involved in many openings and endings in a number of titles (including the Mazinger and Getter series), makes his voice acting debut in the role of the game's main antagonist.