Persona 3 FES is the kind of RPG where the differences in level between various characters can become a problem. Persona 3 has all of the classic causes for this particular problem: the main hero can never leave the team, there are more allies than you can have in the team at one time, there are many advantages to using all of your team members rather than just a minimal number, and team members you are not actively using will not gain any experience points. The problem is further emphasized by the lethality of the game; battles are incredibly deadly even for characters at the appropriate level, and they would be suicidal for a character who has fallen too far behind since all of an ally's abilities are level-dependent. The simple truth is that it is inevitable that some of your allies fall ever more behind in level every time the hero fights a battle, and in addition to being something of a pet peeve of mine, this effect can severely affect the long term viability of a team.
Fortunately, while level gaps are inevitable in Persona 3, the game designers have also provided a pretty good solution to the classic problem: the ability to order your allies to fight Shadows independently of the main hero himself. At any point while exploring Tartarus you can simply order your allies to break off and fight battles on their own, letting the hero sit back and watch as all of the battles are fought for him. Because of this, even though you always control the hero, he does not always have to participate in every battle. Your allies can gain experience without adding to the experience difference between the hero and any other character, and as a result it is possible to make up for any level gap, given enough time. However, "enough time" is the part where another issue arises.
Your allies simply do not earn a lot of experience when they defeat a shadow without the hero's help. They gain some experience, so fixing level gaps is an inevitability, but doing so can take quite a lot of effort. The big problem is that your allies seem to earn far more experience when the hero participates in a battle than when he does not, even though the general rule in the game holds that you gain more experience if fewer people participate in a battle, In truth, an ally fighting alone may earn 20 experience points from a particular enemy, but a team of both that character and the hero would earn 50 experience points from the same enemy. In addition, the amount of experience you allies earn when fighting Shadows without the hero around is incredibly hard to predict, particularly since it is impossible to know what you allies are actually fighting unless the hero intervenes. Because of these factors, correcting level gaps can be a time-consuming hit-or-miss process.
Another problem with this method is that it can be both dull and frustrating. The AI that runs how characters explore the levels of Tartarus is not very good, and combined with the random nature of the dungeon it means that it is impossible to just order your allies to fight Shadows and get a prompt and effective result. An even bigger issue is the fact that your allies simply don't seem to fight very well without you. Even enemies far below the team's level can kill an ally in a single battle and your allies don't ever heal themselves on their own, so you need to constantly run around monitoring their health and healing them when necessary, which can be troublesome in large areas where allies are far apart. Even if things go well, it still involves a lot of standing around waiting for battles to finish. All told, this whole process is almost more trouble than it is worth.
As a whole, the ability to split up your team and fight Shadows individually in Persona 3 would work really well if it was just modified slightly. If it was a little less troublesome and a little more rewarding, it would be a lot more useful. I suppose that the game designers did not want it to be a completely superior choice to normal team combat, particularly since any battle that does not involve the hero will never lead to a Game Over, but I think they might have gone a bit too far in making it a poor choice.