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I don't think there are any rpgs that set out to create an unbalanced system. However, with a team of three or four vs one boss, there are going to be different rules for each side. This really can't be avoided b/c a lot of gameplay in rpgs relies on equipment, levels, and items, which are things that the enemies don't have access to.
The trouble with this is, that even if the developers consider the player's team and the enemies to be equally matched, they don't generally account for all the advantages the player specifically seeks out. Players will level grind, they will buy the best equipment, they will build their characters with the ideal stats, they will focus on the best skills, and they will create strategies to completely counteract everything the boss is capable of.
In this way, SMT IV is like any rpg. The biggest difference is that the favor is initial skewed towards the enemies. The player has to do everything in his or her power to even the playing field. They have to use all the mentioned techniques to have a chance against the enemies' advantage. So really, this game isn't as naturally balanced as other rpgs b/c it doesn't account for the innate differences between the player's team and the enemies. It is only somewhat balanced b/c it requires the player to balance it on their own. And even then, there are some abilities and builds that give the player such a ridiculous advantage that they really can't be killed without the enemies resorting to cheap tactics at times.