D&D is designed as a team game with clear, distinct roles. Indeed, this is deliberately so - those defined roles, and the niche protection that goes with them, means that all the players should get their chance in the spotlight, their chance to do their thing.
But... everyone loves Wolverine and everyone loves Batman, and one of the reasons people like these characters so much is that they're the cool "lone wolf" character. Very often, even when the X-Men or Justice League are doing their thing, that one character will be off pursuing his own agenda. And, sometimes, players want their characters to reflect that. (And, equally, it's not entirely unreasonable to sometimes have a character off on a solo-adventure, if Bob is the only player who shows up. Think of it as the "Iron Man" movie where the regular session is "The Avengers".)
But that niche protection works quite strongly against the use of lone-wolf characters - most difficulty levels are calibrated for a character working as part of a team, and there are a whole bunch of challenges that a lone wolf simply can't tackle. (And, indeed, it's not all that feasible to simply run the character against a lower-level adventure and expect it to compensate - the moment that character hits his first lock, the adventure may well be over!)
So, something I've been noodling over...
The Two Modes of Play
Each character can operate in one of two modes: "team player" or "lone wolf". It should be fairly obvious when he's acting in one or the other - if he's off on a solo mission or side quest, he's a lone wolf; otherwise he's a team player. (He's also a team player if he's acting as a scout or similar - he's still performing a role for the team, he's just not physically located with the team right then.)
There's no action involved in switching modes - the character's circumstances will make one or the other appropriate, and should be used accordingly.
(For ease of transition, it might be a good idea to keep two copies of the character sheet, one for each of the modes. Since the transition effectively changes every modifier used but does so in a predictable way, it's just easier to let the auto-calculating sheet take the strain.)
The Non-proficiency Bonus
Each character has a "non-proficiency bonus". This bonus is added to all rolls for things that the character is not proficient in.
So...
Team Players
When acting as a team player, the character functions exactly as he does now: his Proficiency Bonus is set by his level and is added to all the things he's proficient in; his Non-proficiency Bonus is +0 and so can be ignored.
The one change I would suggest to the way the game plays is to significantly expand the range of things that can be achieved only by a proficient character - when in team player mode, a character can pick a lock only if he's proficient in thieves' tools. That's just about enhancing niche protection - the Rogue picks the locks; the Fighter fights.
Lone Wolves
When acting as a lone wolf, the character functions slightly differently: his Proficiency Bonus is reduced by 1, and is added to all the things he's proficient in; his Non-proficiency Bonus is half of his (reduced) Proficiency Bonus (rounded down), and is added to everything else. And in this mode there are no tasks that are "proficient only" - the character can at least attempt to pick that lock!
(The reason the proficiency bonus is reduced is to avoid the temptation for players to argue they should always be in "lone wolf" mode - if you're in a team, you're better off with the higher bonus. If you want a justification, the character has less to worry about and so can be better focussed on his specialities.)
One More Thing: Hit Dice in Solo Play
When playing in "lone wolf" mode, I'm inclined to suggest that characters should have double the normal hit dice, thus allowing them to heal well in the absence of a Cleric. However, I'm further inclined to suggest that this should really only be for solo adventures, and not for those cases where Batman peels off from the Justice League for his side mission only to rejoin them for the final showdown. So if Bob is the only player to turn up, he gets the extra hit dice; if Bob has his character go off on his own, he doesn't.
Anyway, that's that. For the moment, it's just an idea, though.