The main storyline (to begin with!) are the stories of the nations, Windhurst / San D'Oria / Bastok. These used to be the primary focus until later levels. Then the importance of completing the expansion storylines such as Rise of the Zilart, Chains of Promethia etc. etc. take over due to the importance of unlocking specific content.

Final Fantasy XI was a completionists worst nightmare (or absoloute dream!), there was so many different types of questing content (relative to Job unlocks, area unlocks and even to raise the level cap!). I'll never forget the days and days it took finding the different weather to complete the Carbuncle's Ruby quest.

I think these days when returning to the game - it is important to grind a few levels, then explore the game at you leisure and see where you end up. The storylines in this game are fantastic, its hard to pick a favourite!

I'd save a Crystalline Prophecy, Shantoto's Ascention & Moogle Kupo D'Etat until last though as they didn't have quite the same level as depth.