This is a problem I've been having in general so far as a Game Master; some character classes seem to be designed not for party play, but to be "loners" and shine only in specific situations. Some players like them, some pick them, I just don't know how to "Master" them.
Some examples of my history with said classes:
-
D&D 5th Edition. A player creates a rogue player; he loves stealth scenes, assassination, etc. He notices he's become the "official trap disarmer" of the party, and every now and then he gets to shine in stealth sections, however since half the party wears heavy armors they usually crash the fun for him or he has to go alone, fails some die rolls, and is placed in a very dangerous and life threatening situation that doesn't gets any better. He soons starts hating to be a Rogue because there's not enough chances to be sneaky and cut throats, and he becomes the "skill maid" and trap-damage-eating guy.
-
Pokemon Tabletop United: A player wants to become "too specific" as well and builds a character of the Rider class, so he can Ride on Dragon Pokemon. Tho it fits the game world (since we're playing in a Dynasty Warriors x Pokemon setting), he wants to use his very specific rider combat class every single session, however that also means the prep increases and the things become stale because every single encounter I have to think of another flying rider or he becomes too over powered since the rest of the guys fight in land. Also, he wants only Dragons on his team, so at low levels he has nothing to ride since he doesn't wants land rides, which has made using his whole "Dragon Rider" class very stressful, even if it fits the game world.
-
Anima: Beyond Fantasy: A player creates a scholar, he wants to play the role of the nerd that follows the group of adventurers and writes down everything about their travels while aiding them with her wit and brains. The game is high fantasy action, and what she does every turn is just run, hide, and spend real life hours thinking on what to do since her build means even a rock between her eyes wil lmake her explode in a bloody mess. She still insists to be the "puzzle solver" and "mystery master", so I have to think on puzzles just for her every single game…
We've used the Same Page tool, and as a group we have fun and we really like to play together, however it doesn't stop them from wanting characters that are too specific and require extra planning and solo scenes for them to really shine as the others do, which turns the roleplay into boring because during those scenes, they either become stuck, or want more of that "main character "feel, since there's no way they can really aid the party without getting bored, and sadly, RAW support those characters and I can't tell them "no" because all of them fit my game worlds…
Best Answer
You've run into a common problem - "Party RPGs with non-Party Characters". Same Page Tool can't fix groups who want different things, and it also can't fix game design that works against it's own game premise. You have a few options:
Class Limiting
Games that usually have classes antithetical to their goals usually also have a pretty broad set of class selection, so it's usually not too bad in terms of choice limiting. The other half to deal with is the social contract of your group.
(There's also a subset of gamers out there who deliberately pick the most contrary ideas to what you state the game is about. "Dude, why do you have a Navy Seal character in our game about civilians running from monsters?" Those players are their own problem...)
Building with Limitation in Mind
This is a relatively good option - you can get stuff like "combat rogues" and such that are better designed for situations rather than splitting off. This depends a bit on the system's ability to allow customization or choices within the class system, and also lets players know up front what they need to consider with a character class build.
Non-Party Play and Strong Pacing
If you can run a game which isn't dependent upon a party structure, all those character classes generally work fine as long as their goals and concepts line up. In these kinds of games you need to be able to cut scenes relatively quickly, not spend a lot of time on wasted scenes and the players need to have good goals to aim for.
That said, usually systems that are more mechanically light work better for this than ones attempting to balance out a lot of abilities, though games like Burning Wheel or Blade of the Iron Throne can work fine for it, mostly because the basic resolution systems allow for quick play and give good goal-building tools in the form of Flag mechanics.