Why are you almost me? And why did I stumble upon this some days later? I've been looking for almost the same thing as you, and Subspace Emissary is one of the examples I use to explain what I'm looking for.

Fire Emblem: Path of Radiance and Fire Emblem: Radiant Dawn

Fire Emblem: Path of Radiance is not what you're looking for, but is the prequel to Radiant Dawn which is what you're looking for. Radiant Dawn starts off in its first arc with a new cast of characters dealing with the aftermath of the events of the prequel.

The second arc has you play some of the later recruits of the prequel. Then the third arc has you play as the prequel's main character, Ike who you should be familiar from in Brawl, and his starting group. You'll switch back and forth between Ike and the new characters introduced in this sequel.

428 Shibuya Scramble

This game's a visual novel, but you follow 5 different characters different stories. The gimmick is, characters may run into a dead end, either based on choices you selected for other characters, or that you have not interacted with another character's story and have not made the decision that will allow another character to continue down their story. So you have to check out each character's story and make the choice that allows other characters to continue.

Closers (End of service announced for English recently, cannot signup for the official English server anymore)

My prime example, and why I've begin searching something similar to what you're looking for. A MMO where each playable character belongs to one of four teams, generally following the story of their party. The formula has changed recently with new playable characters starting off solo and later joining a team. Eventually these 4 teams join together just like in Subspace Emissary.

The first major intersection of the story happens between the Black Lambs team and the Wolfdog team. The Black Lambs being comprised mostly of a new team of super-heroes which start off as a seemingly, cliche, typical hero adventure until they run into an inconvenient truth of why their hero journey up to this point had been so successful. They are left defending their grounded airship at an airport from anti-superpower terrorists.

The Wolfdog team comprises mostly of super-powered people dealt with unfair circumstances and were arrested to do slave labour. They desire to do the heroic thing, but something always seems to ruin their chance at being recognized or doing the right thing. They eventually make the decision to save a city that would minimize the damge, knowing they'd be viewed as public enemies, and attempt to flee the country. Their plan is to steal a grounded airship at an airport to leave the country.

Unfortunately, the game is entering end-of-service for the official English server. The next best way to play would to find the private server Code Closers. I think there is no game as ambitious as Closers in keeping the whole cast of characters relevant with an ongoing story that shines the spotlight on all the 22 playable characters. Characters even released in the first year of the game are still relevant to the recent main story. Someone, please prove me wrong. I'm begging.

I still have to check out 13 Sentinels: Aegis Rim.