I just ran a game last night that found the Heroes in Freiburg.  I wanted to develop a way to both allow for a great deal of adventuring, "side quest" potential, the ability to work toward their individual stories, and build out the world.

What I came up with was this:

1.) The local villain's scheme would trigger in 3 days.  I would let them know this time limit almost immediatly via a plot hook in this case, there is a hush-hush conference taking place at the University at the end of the 3 days.  The person they are looking for, in this case the villain (though they don't know he's the villian yet), isn't in the city, but will return by that time.

2.) Each character had 3 actions that they could take in a single day.  Each action was simply to tell me which district they were going to and what they were going to do.  Investigate one of their leads? Engage in their personal story? Investigate hooks from previous "episodes"?  Each thing would take a single action, but I also gave them the opportunity to spend all 3 in a single day to generate Wealth points per the rules.  They also knew that each day they would have to collectively spend 2 Wealth to secure lodgings that were safe, unless they had an advantage that negated this (ie, an Ordained Priest can stay in the Cathedral for free).  They could also take only a single action each day to work on their personal story, if they so desired.  Finally, if they had an Advantage that could help generate wealth (such as Tenure for the University), they had a one-time ability to do so once in the 3 days at the cost of only 1 of their daily actions.

3.) I developed 1-2 "side quest" plot hooks for each district, as well as 1 plot hook related to the "main quest".  Each of these was simple, once or two sentences to build on.  At the start of each day, they had to give me their plans for all 3 actions for that day.  I also told them that if they had to travel to other districts of the city to do their actions, the effects would be diminished due to the extra travel time.  This forced them to both split up and plan their actions within a limited geographical portion of the city.

4.) I addressed the result of each character's actions, in order, running scenes as necessary.  At the end of each "day", they got back together to "debrief" and plan out their next day's actions.  Wash, rince, repeat.

My players loved it.  They said it allowed them to feel like they were working independently towards personal goals along with trying to balance it with collective goals.  The results of their investigations so far have them believing that the villian is actually a great guy, that his rival (a hero who he is trying to corrupt through schemes to get his hands on her research) is probably a horrible person, and when we ended the game, they were leading a mob of dockworkers to assult a warehouse suspected of housing slaves brought in by the ATC for nefarious purposes (which is a "side quest" but which will affect the final showdown with the villian).