I'm going to set up a hypothetical scenario. I've made a traditional JRPG. The first part of the game is a pretty linear affair. Of course because this is a JRPG there are levels to gain, equipment to buy, and spells to learn. Through this linear section the game's difficulty ramps up at a steady pace with the player's level.
There comes a point near the end of the game where the world "opens up." The player has the choice to go straight to the final dungeon and complete the game OR complete the dozens of side quests that are available. Of course these side quests have rewards for the player such as more powerful weapons, equipment, and spells.
Now I have a dilemma. One player could skip all the side quests and go straight to the final dungeon. Another player could complete all of the side quests before attacking the final dungeon. These two players would have a massive difference in power levels.
How do I balance the final dungeon so that both players get an adequate challenge?