The reason why there always seems to be only room for one protagonist in a game's story is because it is inherit in the medium that there is just one "real" protagonist: The player. The player will always feel that they are the main character in the story, no matter how well-developed the personality of the actual player-character is. You can tell by the way players describe their experiences in games. They never say something like "I walked protagonist to the dungeon and had him kill the boss" they say "I went to the dungeon and killed the boss". This is why changing the viewpoint character feels so weird in games. You used to be one person and now you are suddenly a completely different person.
However, when you want a plot where multiple characters share equal amounts of attention, then there is a frequently used technique for that: Make the protagonist as unimportant and bland as possible so they don't steal the spotlight from the characters you actually want to focus on. Acknowledge that the player-character exists by having characters talk to them (which means having them talk directly to the player), but don't show them on-screen, don't have them talk and don't give them any characterization and most importantly don't give them any personal story-arcs. You might not even have them participate in the game mechanics. You could, for example, make the player the team commander who makes all the decisions (as players tend to do in RPGs), but doesn't get involved in combat directly.
Now with the PC out of the way, you can make the secondary characters as colorful and interesting as you want without them getting overshadowed. But don't overdo the number of plot-relevant characters in your game. The amount of characters the player can keep track of in a game will always be lower than in non-interactive media. The reason is that in non-interactive media, the reader/viewer/listener pays 100% attention to the story. In a game, the player's attention is divided between story and mechanics. (good game designers try to blur the lines between story and mechanics so there is no longer a competition between the two, but it isn't always possible to do this, especially if you don't want to leave the confines of a well-established classic genre like JRPGs)
So when you have over about a dozen playable characters, no player will be able to bond with all of them and in the end they will end up bonding with none of them. That means the budget you spent on the individual storylines will be wasted. So either keep the number of characters low, or have a clear distinction between a few "A list" characters who get detailed backgrounds and personal plots and a large pool of "B list" characters who don't.
Regarding creating a combat system which allows a large number of characters to get screentime:
The easiest would be simply to design a combat system which supports a very large player-party. Instead of the typical JRPG combat system with two parties on opposite sides exchanging attacks you might want to go for a Strategy-RPG combat system with grid-based movement and complex terrain (Disgaea, Final Fantasy Tactics, Fire Emblem...).
But if you want to stick to the JRPG combat system with just about 4 characters at once, then you need to encourage the player to switch their party members frequently.
- Add a fatigue mechanic. The most common fatigue mechanic are MP points. Force the player to spend MP even in trivial battles and give very few opportunities to recover MP points between battles. That will force the player to replace characters when they run out of MP. Fatigue mechanics can appear in different ways than just MP points. Common examples are ammo count, Vancian magic systems or literal fatigue represented with temporary stat decreases.
- Make characters highly specialized and add a lot of battles specifically tailored for specific characters. When even the most balanced 4 character party can not win every battle in the game, then players will have to change their party composition regularly.
- Encourage switching party members even while in combat. An easy way to do this is by making in-combat healing and reviving expensive and in-combat party switching cheap. Players get encouraged to replace casualties with less used characters. That way a hard boss battle won't be won by burning through almost all healing items but rather by burning through the whole party roster. Allowing to switch party composition easily during combat is also important to avoid frustration when you follow the previous point (highly specialized battles).
But even when you encourage party rotation a lot, it might still occur that one or two characters slip past the player's attention, fall so far behind that getting them back to the average level of the party becomes a chore (or even mechanically impossible) and they end up getting ignored for the rest of the game. Possible workarounds are:
- Keep the progression curve relatively flat, so characters who fall a few levels behind are still effective.
- Whenever the main party gains exp, also give xx% of those exp points to the unused characters so they don't fall behind.
- Encourage players to backtrack and revisit older locations with easier battles. This presents a good opportunity to level up weaker characters.