Maintaining the storyline
If the main objective is to save the world, why on earth (or whatever planet) would you want to rescue BOB.
BOB (or his family and friends) would have to persude us to rescue him.
In some way (yet be more stile than my example) you'd have to persude the player to rescue BOB because it would help you save the world.
Apart from this is a RPG. So you can put 'rescue BOB' in as a sub quest.
But if your game has no actual apparrent objective, you have to make the next step logical.
fench a pale of water, save the universe?, eat lunch, go home.
E.G. FF7 had no real one objective, and to be honest was it save the world, stop Sephorith (maybe by letting him help us), stop that evil power company or what?
The only thing that really tells you is the end baddie. (apart from the ending in FF7 kind of confused you more)
Don't change the storyline half way through.
Remember:- It's your RPG so just make it so you like it, and therefore other people like-you will also like it.