This is similar to Oblivion. If you just go through the main quest in Oblivion, you will only perform about 10% of the quests in the game.
It's important to realize that these are *not* linear RPGs... they're open-world variations. As such, most of the gaming occurs outside the "main" quest. That's why completing the main quest in Oblivion doesn't actually end the game... you get a special set of armor for completing the questline, then you can just keep playing and do the 90% of what's left.
This probably drives to distraction people who prefer a fixed storyline, but for those who like openworld conquest (World of Warcraft comes to mind), this is a very good way to structure the game.
In summary, this is likely a non-issue with Fable 2.